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tiledb: init at 1.6.2 #67187

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commented Aug 21, 2019

Motivation for this change
Things done
  • Tested using sandboxing (nix.useSandbox on NixOS, or option sandbox in nix.conf on non-NixOS)
  • Built on platform(s)
    • NixOS
    • macOS
    • other Linux distributions
  • Tested via one or more NixOS test(s) if existing and applicable for the change (look inside nixos/tests)
  • Tested compilation of all pkgs that depend on this change using nix-shell -p nix-review --run "nix-review wip"
  • Tested execution of all binary files (usually in ./result/bin/)
  • Determined the impact on package closure size (by running nix path-info -S before and after)
  • Ensured that relevant documentation is up to date
  • Fits CONTRIBUTING.md.
Notify maintainers

cc @CMCDragonkai

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commented Aug 21, 2019

We need help to figure out how to build the tiledb documentation. https://github.com/Intel-HLS/TileDB/wiki/Building-TileDB#step-8---build-tiledb and also how to run its gtest for the checkPhase. Anybody know how to do this?

@CMCDragonkai CMCDragonkai referenced this pull request Aug 21, 2019
@stavrospapadopoulos

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commented Aug 21, 2019

Just FYI, the official TileDB is maintained at https://github.com/TileDB-Inc/TileDB. We'd be happy to help with documentation and tests.

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essentially, i would do this:

Also, python and gtest (they use catch) aren't needed. They might be needed for the bindings, but for the base .so, you dont need it.

tiledb expression
{ stdenv, fetchFromGitHub
, boost
, bzip2
, catch2
, clang-tools
, cmake
, doxygen
, libpqxx
, lz4
, openssl
, spdlog_0
, tbb
, zlib
, zstd
}:

stdenv.mkDerivation rec {
  name = "tiledb";
  version = "1.5.1";

  src = fetchFromGitHub {
    owner = "TileDB-Inc";
    repo = "TileDB";
    rev = version;
    sha256 = "0ky0dcv1w1jn1cjn3819aq9xyd2wg80aagf2flxmd916flgr9zjl";
  };

  nativeBuildInputs = [ clang-tools cmake doxygen ];

  buildInputs = [ catch2 zlib lz4 bzip2 zstd spdlog_0 tbb openssl boost libpqxx ];

  # emulate the process of pulling catch down
  postPatch = ''
    mkdir -p build/externals/src/ep_catch
    ln -sf ${catch2}/include/catch2 build/externals/src/ep_catch/single_include
  '';

  makeTarget = "tiledb";
  installTargets = [ "-C tiledb install" ];

  meta = with stdenv.lib; {
    description = "TileDB allows you to manage the massive dense and sparse multi-dimensional array data";
    homepage = https://github.com/TileDB-Inc/TileDB;
    license = licenses.mit;
    maintainers = with maintainers; [ rakesh4g ];
  };
}

nativeBuildInputs = [clang-tools doxygen gtest];

buildInputs = [cmake catch2 zlib lz4 bzip2 zstd spdlog_0 tbb openssl boost libpqxx python ];

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jonringer Aug 21, 2019

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whitespace and move cmake to nativeBuildInputs. python could probably be moved too if it's not needed at runtime.

Suggested change
buildInputs = [cmake catch2 zlib lz4 bzip2 zstd spdlog_0 tbb openssl boost libpqxx python ];
buildInputs = [ catch2 zlib lz4 bzip2 zstd spdlog_0 tbb openssl boost libpqxx python ];

outputs = ["out"];

nativeBuildInputs = [clang-tools doxygen gtest];

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jonringer Aug 21, 2019

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whitespace, and add cmake

Suggested change
nativeBuildInputs = [clang-tools doxygen gtest];
nativeBuildInputs = [ clang-tools cmake doxygen gtest ];

makeTarget = "tiledb";

outputs = ["out"];

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jonringer Aug 21, 2019

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Having a single output called "$out" is the default, you can remove

Suggested change
outputs = ["out"];
cmakeFlags = [
"-DCATCH_INCLUDE_DIR=${catch2}"
# "-DTILEDB_SUPERBUILD=OFF"
# "-DINCLUDE_DIR=${clang-tools}/bin"

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jonringer Aug 21, 2019

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let nix take care of setting those things like include, library, and other common dirs.

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CMCDragonkai Aug 23, 2019

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Which ones are needed and which ones are not?

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commented Aug 21, 2019

We need help to figure out how to build the tiledb documentation. https://github.com/Intel-HLS/TileDB/wiki/Building-TileDB#step-8---build-tiledb and also how to run its gtest for the checkPhase. Anybody know how to do this?

for the docs:

preInstall = ''
  make doc
'';

for the gtest, no idea

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commented Aug 22, 2019

We need help to figure out how to build the tiledb documentation. https://github.com/Intel-HLS/TileDB/wiki/Building-TileDB#step-8---build-tiledb and also how to run its gtest for the checkPhase. Anybody know how to do this?

for the docs:

preInstall = ''
  make doc
'';

for the gtest, no idea

Thanks @jonringer , Just used check in place of doc. It is triggering test build for tiledb. Though it is failing for other reasons.

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commented Aug 22, 2019

Just FYI, the official TileDB is maintained at https://github.com/TileDB-Inc/TileDB. We'd be happy to help with documentation and tests.

Thanks @stavrospapadopoulos ,

We have raised the issue at: https://github.com/TileDB-Inc/TileDB/issues/1369

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commented Aug 22, 2019

Hello, Tyler from TileDB here. Unless there is a reason otherwise, we recommend you update your package to the latest stable release of TileDB, version 1.6.2. Now that major release 1.6 is available, bugfixes and support for older releases (such as 1.5.1) will be minimal.

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commented Aug 22, 2019

@tdenniston Thanks for your response. We had initially tried with tiledb 1.6.2 only. But we were stuck at tiledb shared library build itself. We had to manually include map file in one or two files to build library itself.this is similar to TileDB-Inc/TileDB#1312 so we later moved back to version 1.5.1.

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commented Aug 22, 2019

@Rakesh4G we'd like to help you get the 1.6.2 package building. Could you please tell us more information about the 1.6.2 build errors? We will investigate whether it is possible to do a 1.6.3 release to address your issues.

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commented Aug 23, 2019

@tdenniston I think the errors he's referring to is here: TileDB-Inc/TileDB#1312

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commented Aug 23, 2019

Hi @tdenniston , Please also find attached the error log from my machine.
[ 51%] Building CXX object tiledb/CMakeFiles/TILEDB_CORE_OBJECTS.dir/sm/kv/kv.cc.o In file included from /build/TileDB-1208899/tiledb/../tiledb/sm/rtree/rtree.h:44:0, from /build/TileDB-1208899/tiledb/../tiledb/sm/fragment/fragment_metadata.h:41, from /build/TileDB-1208899/tiledb/sm/fragment/fragment_metadata.cc:34: /build/TileDB-1208899/tiledb/../tiledb/sm/subarray/subarray.h:529:8: error: 'map' in namespace 'std' does not name a template type std::map<std::vector<uint8_t>, size_t> tile_coords_map_; ^~~
tiledb-error_1.6.2.txt

Used Tiledb is :

   name = "tiledb";
    version = "1.6.2";
    url = "https://github.com/TileDB-Inc/TileDB";
    rev = "12088997fd4a72db6d9ee726c493e73ea38fb67d";
    sha256 = "sha256:0j0f2jmaxv4idywk3wxvziv69aqizi0z8kd54qi4rwnw2b6w3nsr";

Thanks.

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commented Aug 23, 2019

@Rakesh4G if possible could you please try building the TileDB branch at https://github.com/TileDB-Inc/TileDB/tree/ttd/test-missing-include-fix? Commit hash 21279ea5a24cabc60d0ab6c75ad0e19db6004967. The branch is based off of TileDB 1.6.2 and if it fixes the build issue for you, we will include it in release 1.6.3.

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commented Aug 26, 2019

Hi @tdenniston , After using the patch now we are reaching a point where tiledb library is building. But the build error for tiledb_unit is same as before. please see the attached file
tiledb_unit-error_1.6.2_patch.txt

/build/TileDB-21279ea/test/src/unit-capi-consolidation.cc:2946:7: error: unused variable 'has_key' [-Werror=unused-variable]
   int has_key;
       ^~~~~~~
cc1plus: all warnings being treated as errors
make[7]: *** [test/CMakeFiles/tiledb_unit.dir/build.make:193: test/CMakeFiles/tiledb_unit.dir/src/unit-capi-consolidation.cc.o] Error 1

Thanks.

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commented Aug 26, 2019

@Rakesh4G I've pushed a new commit to the same branch (hash 45e7e874570791a23d9c7586f6c08853daaa548c) that should fix the unit test build errors.

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commented Aug 26, 2019

Hi @tdenniston , Thanks. with this now it moves ahead but stops again in

unit-capi-sparse_array.cc:1958:15: error: unused variable 'attributes' [-Werror=unused-variable] const char* attributes[] = {"a2", TILEDB_COORDS};

[ 68%] Building CXX object test/CMakeFiles/tiledb_unit.dir/src/unit-capi-sparse_array.cc.o /build/TileDB-45e7e87/test/src/unit-capi-sparse_array.cc: In member function 'void SparseArrayFx::check_invalid_offsets(const string&)': /build/TileDB-45e7e87/test/src/unit-capi-sparse_array.cc:1958:15: error: unused variable 'attributes' [-Werror=unused-variable] const char* attributes[] = {"a2", TILEDB_COORDS}; ^~~~~~~~~~ cc1plus: all warnings being treated as errors make[7]: *** [test/CMakeFiles/tiledb_unit.dir/build.make:375: test/CMakeFiles/tiledb_unit.dir/src/unit-capi-sparse_array.cc.o] Error 1 make[6]: *** [CMakeFiles/Makefile2:2207: test/CMakeFiles/tiledb_unit.dir/all] Error 2 make[5]: *** [CMakeFiles/Makefile2:2182: test/CMakeFiles/check.dir/rule] Error 2 make[4]: *** [Makefile:942: check] Error 2 make[3]: *** [CMakeFiles/check.dir/build.make:57: CMakeFiles/check] Error 2 make[2]: *** [CMakeFiles/Makefile2:174: CMakeFiles/check.dir/all] Error 2 make[1]: *** [CMakeFiles/Makefile2:181: CMakeFiles/check.dir/rule] Error 2 make: *** [Makefile:157: check] Error 2 builder for '/nix/store/k2jnzv30c6yvrmzc1djbszh92qi4a6mf-tiledb.drv' failed with exit code 2 error: build of '/nix/store/k2jnzv30c6yvrmzc1djbszh92qi4a6mf-tiledb.drv' failed

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commented Aug 26, 2019

@Rakesh4G I've pushed another update. Would you mind telling me your toolchain version and compiler flags? We have CI checks in place to prevent these errors, but our CI did not find these unused variables.

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commented Aug 27, 2019

The toolchain would be whatever is supplied by the standard environment in Nix. So that would be the current master's gcc/clang? Nix is pretty strict for its compiler flags by default.

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commented Aug 27, 2019

@tdenniston full configure log when I attempt to build this

cmake flags: -DCMAKE_FIND_PACKAGE_NO_SYSTEM_PACKAGE_REGISTRY=ON -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_BUILD_TYPE=Release -DCMAKE_SKIP_BUILD_RPATH=ON -DBUILD_TESTING=OFF -DCMAKE_INSTALL_LOCALEDIR=/nix/store/7hgm4n1iprbdlpmv1nhvzbd4kk9g67kv-tiledb/share/locale -DCMAKE_INSTALL_LIBEXECDIR=/nix/store/7hgm4n1iprbdlpmv1nhvzbd4kk9g67kv-tiledb/libexec -DCMAKE_INSTALL_LIBDIR=/nix/store/7hgm4n1iprbdlpmv1nhvzbd4kk9g67kv-tiledb/lib -DCMAKE_INSTALL_DOCDIR=/nix/store/7hgm4n1iprbdlpmv1nhvzbd4kk9g67kv-tiledb/share/doc/ -DCMAKE_INSTALL_INFODIR=/nix/store/7hgm4n1iprbdlpmv1nhvzbd4kk9g67kv-tiledb/share/info -DCMAKE_INSTALL_MANDIR=/nix/store/7hgm4n1iprbdlpmv1nhvzbd4kk9g67kv-tiledb/share/man -DCMAKE_INSTALL_OLDINCLUDEDIR=/nix/store/7hgm4n1iprbdlpmv1nhvzbd4kk9g67kv-tiledb/include -DCMAKE_INSTALL_INCLUDEDIR=/nix/store/7hgm4n1iprbdlpmv1nhvzbd4kk9g67kv-tiledb/include -DCMAKE_INSTALL_SBINDIR=/nix/store/7hgm4n1iprbdlpmv1nhvzbd4kk9g67kv-tiledb/sbin -DCMAKE_INSTALL_BINDIR=/nix/store/7hgm4n1iprbdlpmv1nhvzbd4kk9g67kv-tiledb/bin -DCMAKE_INSTALL_NAME_DIR=/nix/store/7hgm4n1iprbdlpmv1nhvzbd4kk9g67kv-tiledb/lib -DCMAKE_POLICY_DEFAULT_CMP0025=NEW -DCMAKE_OSX_DEPLOYMENT_TARGET= -DCMAKE_OSX_SYSROOT= -DCMAKE_FIND_FRAMEWORK=last -DCMAKE_STRIP=/nix/store/mgdjnsrkqgmxqjaqaxgqyqm7fwyi96fk-binutils-2.31.1/bin/strip -DCMAKE_RANLIB=/nix/store/mgdjnsrkqgmxqjaqaxgqyqm7fwyi96fk-binutils-2.31.1/bin/ranlib -DCMAKE_AR=/nix/store/mgdjnsrkqgmxqjaqaxgqyqm7fwyi96fk-binutils-2.31.1/bin/ar -DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=g++ -DCMAKE_INSTALL_PREFIX=/nix/store/7hgm4n1iprbdlpmv1nhvzbd4kk9g67kv-tiledb
-- The C compiler identification is GNU 7.4.0
-- The CXX compiler identification is GNU 7.4.0
-- Check for working C compiler: /nix/store/hpzj855nkgjvg58nrhq4910sb9q3kss1-gcc-wrapper-7.4.0/bin/gcc
-- Check for working C compiler: /nix/store/hpzj855nkgjvg58nrhq4910sb9q3kss1-gcc-wrapper-7.4.0/bin/gcc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /nix/store/hpzj855nkgjvg58nrhq4910sb9q3kss1-gcc-wrapper-7.4.0/bin/g++
-- Check for working CXX compiler: /nix/store/hpzj855nkgjvg58nrhq4910sb9q3kss1-gcc-wrapper-7.4.0/bin/g++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Starting TileDB superbuild.
-- Found Bzip2: /nix/store/g8al6vdf21mgfi5774qx6r6cil1j7zr8-bzip2-1.0.6.0.1/lib/libbz2.so
-- Found LZ4: /nix/store/6s41b1kn253k4b8dwlyai76d1cazxcdm-lz4-1.9.1/lib/liblz4.so
-- Found Spdlog: /nix/store/3yw2kclpsx02b9hx6ssbbrwlixf5pdi5-spdlog-0.17.0/include
-- Found Zlib: /nix/store/w3wqang215is14xqajycbxmd52b44qkw-zlib-1.2.11/lib/libz.so
-- Found Zstd: /nix/store/aydp0jd0yvg5r5ynsqv1b6i67w736afv-zstd-1.4.1/lib/libzstd.so
-- Found OpenSSL: /nix/store/1g9n3mxrawawa5p9mv8g2baaxjvdg2ag-openssl-1.0.2s/lib/libssl.so /nix/store/1g9n3mxrawawa5p9mv8g2baaxjvdg2ag-openssl-1.0.2s/lib/libcrypto.so
-- Found TBB: /nix/store/g7p34bn41bzmjfi1kabkks8md9bdjx1p-tbb-2019_U8/lib/libtbb.so
-- Found TBB imported target: TBB::tbb
-- searching for catch in /build/TileDB-7236bb2/build/externals/src
-- Found Catch: /build/TileDB-7236bb2/build/externals/src/ep_catch/single_include
-- Not found clang-tidy
-- Not found clang-format
-- Found Doxygen: /nix/store/4b4pxa2l331s2z1qd3wh50a30nw22swn-doxygen-1.8.15/bin/doxygen (found version "1.8.15") found components:  doxygen missing components:  dot
-- Install prefix is /nix/store/7hgm4n1iprbdlpmv1nhvzbd4kk9g67kv-tiledb
-- Configuring done
-- Generating done
@Rakesh4G Rakesh4G changed the title tiledb: init at 1.5.1 tiledb: init at 1.6.2 Aug 28, 2019
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commented Aug 30, 2019

Hi @tdenniston , Did you get a chance to look into the tiledb test failures? Thanks.

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commented Aug 30, 2019

Hello,

So far I've been unable to reproduce your test failures. Here is what I tried (on two EC2 instances):

curl https://nixos.org/nix/install > install-nix
sh install-nix  # Had to do this twice, first time segfaulted.
git clone https://github.com/NixOS/nixpkgs.git
cd nixpkgs
git fetch origin pull/67187/head:tiledb
git checkout tiledb
nix-build -A tiledb

System was Ubuntu 18.04:

$ cat /etc/lsb-release
DISTRIB_ID=Ubuntu
DISTRIB_RELEASE=18.04
DISTRIB_CODENAME=bionic
DISTRIB_DESCRIPTION="Ubuntu 18.04.2 LTS"
$ uname -a
Linux ip-172-31-11-24 4.15.0-1045-aws #47-Ubuntu SMP Fri Aug 2 13:50:30 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
$ lscpu | grep 'Model name'
Model name:          Intel(R) Xeon(R) Platinum 8175M CPU @ 2.50GHz

and separately I tried also on an AMD instance (AWS m5a type):

$ uname -a
Linux ip-172-31-91-93 4.15.0-1044-aws #46-Ubuntu SMP Thu Jul 4 13:38:28 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
$ lscpu | grep 'Model name'
Model name:          AMD EPYC 7571

I also tried locally mounting the build directory via NFS:

sudo mount localhost:/home /mnt/nfshome
cd /mnt/nfshome/ubuntu/nixpkgs
nix-build -A tiledb

None of the above resulted in the test failures you are seeing. What am I missing?

@Rakesh4G Rakesh4G referenced this pull request Sep 2, 2019
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commented Sep 2, 2019

Hi @tdenniston ,
I am trying to put together some details from my system:
File system : ZFS

nixos-version
19.09.git.57c3da07eb8M (Loris)

uname -a
Linux formbay-ml-2-C 4.19.46 #1 NixOS SMP Sat May 25 16:23:48 UTC 2019 x86_64 GNU/Linux

command used for building tiledb
nix-env -f /Projects/nixpkgs -iA tiledb
where /Projects/nixpkgs is path of nixpkgs

I am also attaching env output from my system in case you are able to find any odds.
env_output.txt

Also I have tried to use command
nix-build -A tiledb

but errors are still there.

Also there is one weird behaviour observed for tiledb_unit. I am getting different test results on different runs.

Only 1 test failure :
tiledb_unit_run_error_only_1_Fail.txt

11 Test Failures :
tiledb_unit_run_error_11_Fail.txt

Thanks.

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commented Sep 2, 2019

I tried the same steps as @tdenniston in this comment on two different systems:

Both runs result in 100% pass for tiledb_unit. (however note that the install step fails because the install target created by cmake is called install-tiledb rather than install).

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commented Sep 3, 2019

Hi @ihnorton @tdenniston ,
If it is possible for you to share the build/run logs. We would try to compare it with our system logs to see if there is any mismatch in environment settings. Thanks.

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commented Sep 3, 2019

log below

(tiledb):~/scratch/nix-build-20190830/nixpkgs$ nix-build -A tiledb
these derivations will be built:
  /nix/store/57aaf1dz5bs7h0ksymqjafvn6qi4160l-TileDB-0eb1eba.drv
  /nix/store/bygp9ffv7wv35lcw0af6h708ajaqhbwk-tiledb.drv
these paths will be fetched (283.32 MiB download, 1619.32 MiB unpacked):
  /nix/store/0acqnzib0xlk02f6qy5mnbd8zgjwh3i7-stdenv-linux
  /nix/store/0rmgggcsig05ryqga770bhc9jf99ip3w-ncurses-6.1-20190112-dev
  /nix/store/14yd5rgja0c8zcd4x72ylizn06dh8m4p-libxml2-2.9.9-bin
  /nix/store/1g9n3mxrawawa5p9mv8g2baaxjvdg2ag-openssl-1.0.2s
  /nix/store/1ky9xdc2gkx9rkdqxs6wsnxwf96byl2v-curl-7.65.3
  /nix/store/1m5w1wnfw5iffnpqfrq7svqwi7z13245-gtest-1.8.1-dev
  /nix/store/1mvglgr1gmfnc3qzxldwfn3g01aknn0f-libgcrypt-1.8.4
  /nix/store/1nrimml11nlg7spkrq0ki1337cjc4222-expat-2.2.7
  /nix/store/1x6b6pax9n5vrjw8hvgqq2wpzssdi5z7-catch2-2.8.0
  /nix/store/1xdhbl1qwavq6fsq5as75g2sigb5p0vi-libuv-1.30.1
  /nix/store/1y0svafx9vypz073nqnq7qlhssrflqr4-pcre-8.43
  /nix/store/2kxncjc6rzlqwqllgjmifskpf2irq5k5-gdbm-1.18.1
  /nix/store/2vbkm6a57fyxik8ladnlchmi10r95rrp-libedit-20190324-3.1
  /nix/store/301bvcqxhs8f2kfqmpyi6qay4zybxgyz-llvm-8.0.1-lib
  /nix/store/3142pwpbixhxfhp4dlbdlf8zabf7vn7m-perl5.28.2-CGI-Fast-2.15
  /nix/store/3njdywpyqns813nc5f2padax9vsdvyl5-gettext-0.19.8.1
  /nix/store/3r3wp8pnfqjr9fz53hpf5mr2mwpba4p0-nss-cacert-3.44.1
  /nix/store/3sfg7a86kqds0axwdlj40lwnscxhcc6m-libarchive-3.4.0-lib
  /nix/store/3wn28aim9k0ccjdz763d23fb71n09qrc-libcap-2.27-lib
  /nix/store/3yw2kclpsx02b9hx6ssbbrwlixf5pdi5-spdlog-0.17.0
  /nix/store/3yx531sm6vmlmcjlxjv9n7h9scr0mlnl-git-2.22.0
  /nix/store/434g94la6frs13apdc2pxbfl6z8q6g6x-perl5.28.2-FCGI-ProcManager-0.28
  /nix/store/4b4pxa2l331s2z1qd3wh50a30nw22swn-doxygen-1.8.15
  /nix/store/4i4sha6xrchsghg8gpx67n2lwynbkmrm-perl5.28.2-libwww-perl-6.39
  /nix/store/4rqb1bg5dqccrfrk0x7d0kc8f7l4rwqk-libkrb5-1.17
  /nix/store/5bbll8n7rgyrlb39fyl2r2i30vnb7pxc-perl5.28.2-IO-HTML-1.001
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copying path '/nix/store/byjx6iw5ym2pfz8zn6vmrx7sd0rhyw25-perl5.28.2-URI-1.76' from 'https://cache.nixos.org'...
copying path '/nix/store/rv1qylp261il97imdcvm7fq1nyfvv5pg-perl5.28.2-Test-Fatal-0.014' from 'https://cache.nixos.org'...
copying path '/nix/store/wvq667rhfjpv80arjjkyf6ykykjwwaxz-perl5.28.2-HTTP-Message-6.18' from 'https://cache.nixos.org'...
copying path '/nix/store/61wd2jrkkm7waakpb8n55spz84cszssk-perl5.28.2-Net-HTTP-6.19' from 'https://cache.nixos.org'...
copying path '/nix/store/6zj9x7fzbqcwsv05ha8252bqfkw099hi-perl5.28.2-HTTP-Cookies-6.04' from 'https://cache.nixos.org'...
copying path '/nix/store/pdpmvb6i4kcgh58wyqam2q5fixam8z3a-perl5.28.2-HTTP-Daemon-6.01' from 'https://cache.nixos.org'...
copying path '/nix/store/5saq6gj32zfry4d2p5gaial8dhhha4i3-perl5.28.2-HTTP-Negotiate-6.01' from 'https://cache.nixos.org'...
copying path '/nix/store/aksdfn4y06fwg153mi75jd5k3h8p1mdq-perl5.28.2-WWW-RobotRules-6.02' from 'https://cache.nixos.org'...
copying path '/nix/store/jv5dfbr6dkm033ipnp6avkyxwbnbh8vv-readline-6.3p08' from 'https://cache.nixos.org'...
copying path '/nix/store/4i4sha6xrchsghg8gpx67n2lwynbkmrm-perl5.28.2-libwww-perl-6.39' from 'https://cache.nixos.org'...
copying path '/nix/store/76p0gykww47qqf6skwr7c5n5jgbw68m2-rhash-1.3.8' from 'https://cache.nixos.org'...
copying path '/nix/store/3yw2kclpsx02b9hx6ssbbrwlixf5pdi5-spdlog-0.17.0' from 'https://cache.nixos.org'...
copying path '/nix/store/g7p34bn41bzmjfi1kabkks8md9bdjx1p-tbb-2019_U8' from 'https://cache.nixos.org'...
copying path '/nix/store/p6znrsqrj9fg8hgqyba4z0993raxphyd-tzdata-2019a' from 'https://cache.nixos.org'...
copying path '/nix/store/ji9kpgmbddkv2l2szzjfqinhja2322k0-xz-5.2.4' from 'https://cache.nixos.org'...
copying path '/nix/store/w3wqang215is14xqajycbxmd52b44qkw-zlib-1.2.11' from 'https://cache.nixos.org'...
copying path '/nix/store/nj1v1qgmnmfqjf65hwqsgdzq8qdxf4cy-systemd-242-lib' from 'https://cache.nixos.org'...
copying path '/nix/store/mgdjnsrkqgmxqjaqaxgqyqm7fwyi96fk-binutils-2.31.1' from 'https://cache.nixos.org'...
copying path '/nix/store/mzkvw3fvnp0whkkl9znff6mxwac5xjsi-boost-1.67.0' from 'https://cache.nixos.org'...
copying path '/nix/store/hsi8wy263vimgvr4nf2hvf9gx661qkvj-binutils-wrapper-2.31.1' from 'https://cache.nixos.org'...
copying path '/nix/store/9yixdi8b04i8py2x9la0qn32cxqb57cy-boost-1.67.0-dev' from 'https://cache.nixos.org'...
copying path '/nix/store/izllmdcc68inlk7csiaqz5rkc5iy7wcm-cracklib-2.9.7' from 'https://cache.nixos.org'...
copying path '/nix/store/wr5dlcw1asw8dwgm4bwjmga8f52m5lfx-gcc-7.4.0' from 'https://cache.nixos.org'...
copying path '/nix/store/p1fr2qchyyql9k1blh9xjkbvi8lhi642-libssh2-1.9.0' from 'https://cache.nixos.org'...
copying path '/nix/store/hpzj855nkgjvg58nrhq4910sb9q3kss1-gcc-wrapper-7.4.0' from 'https://cache.nixos.org'...
copying path '/nix/store/1ky9xdc2gkx9rkdqxs6wsnxwf96byl2v-curl-7.65.3' from 'https://cache.nixos.org'...
copying path '/nix/store/jwyny3q9jrlk4jhvhchavpzw8hcy6x1p-libxml2-2.9.9' from 'https://cache.nixos.org'...
copying path '/nix/store/virwdk17hb952krz8hhkg2jypwa0a6jk-linux-pam-1.3.1' from 'https://cache.nixos.org'...
copying path '/nix/store/3sfg7a86kqds0axwdlj40lwnscxhcc6m-libarchive-3.4.0-lib' from 'https://cache.nixos.org'...
copying path '/nix/store/14yd5rgja0c8zcd4x72ylizn06dh8m4p-libxml2-2.9.9-bin' from 'https://cache.nixos.org'...
copying path '/nix/store/rlp98mmbvp008720p25k73w2khzs9rzn-cmake-3.14.5' from 'https://cache.nixos.org'...
copying path '/nix/store/301bvcqxhs8f2kfqmpyi6qay4zybxgyz-llvm-8.0.1-lib' from 'https://cache.nixos.org'...
copying path '/nix/store/d6pakidxdm4pdig3l11cwl1l0sgd6hvl-openssh-7.9p1' from 'https://cache.nixos.org'...
copying path '/nix/store/cvq4nwkyiw8imdh2qgjvgdp8vjqqr115-clang-8.0.1-lib' from 'https://cache.nixos.org'...
copying path '/nix/store/3yx531sm6vmlmcjlxjv9n7h9scr0mlnl-git-2.22.0' from 'https://cache.nixos.org'...
copying path '/nix/store/xxhn5cqgq5aa1237avjv951alpjiyhrc-postgresql-9.6.15-lib' from 'https://cache.nixos.org'...
copying path '/nix/store/fb5zh67kkzv9qydxbc0qhbnhiq5vrn7l-sqlite-3.28.0' from 'https://cache.nixos.org'...
copying path '/nix/store/7y1afcqr7zw2p8cz7yhkyf3xb3ss1f32-xz-5.2.4-bin' from 'https://cache.nixos.org'...
copying path '/nix/store/whb8vd9pmssdmzhqffzkc3vz6ih3q1yk-python-2.7.16' from 'https://cache.nixos.org'...
copying path '/nix/store/0acqnzib0xlk02f6qy5mnbd8zgjwh3i7-stdenv-linux' from 'https://cache.nixos.org'...
copying path '/nix/store/db3j7hf0w0za4c3zk470gk2ang7vs9zw-libxml2-2.9.9-py' from 'https://cache.nixos.org'...
copying path '/nix/store/k0d4kbgja96dw0dibzmi75dy10qxg8hz-stdenv-linux' from 'https://cache.nixos.org'...
copying path '/nix/store/9dh8v2v3lvm79b6c0rxh50ps3s311dwk-zlib-1.2.11-dev' from 'https://cache.nixos.org'...
copying path '/nix/store/aydp0jd0yvg5r5ynsqv1b6i67w736afv-zstd-1.4.1' from 'https://cache.nixos.org'...
copying path '/nix/store/w2k77j0a8vpdqsnhb7yczcz8lh6h51yp-libxml2-2.9.9-dev' from 'https://cache.nixos.org'...
copying path '/nix/store/95avhjqs8rgmyydfk2v4iq5z0054mlhr-llvm-8.0.1' from 'https://cache.nixos.org'...
copying path '/nix/store/jmx9vwiq65jbdh2pi70naixd9vqhys60-postgresql-9.6.15' from 'https://cache.nixos.org'...
copying path '/nix/store/grmdb3x5p2lpyk0iwpjm96f01sbvny7p-clang-8.0.1' from 'https://cache.nixos.org'...
copying path '/nix/store/60gajqqadlyhnn65qzk5wjx9rvcr6d3q-libpqxx-6.4.5' from 'https://cache.nixos.org'...
copying path '/nix/store/syx9nf42rissv6hwfrkmwklqqxfl682i-clang-tools-8.0.1' from 'https://cache.nixos.org'...
building '/nix/store/57aaf1dz5bs7h0ksymqjafvn6qi4160l-TileDB-0eb1eba.drv'...
exporting https://github.com/TileDB-Inc/TileDB (rev 0eb1eba7a9ff0ada0165bd61c84239bec9cf0f00) into /nix/store/phrhd49k173kw7bnrldzif84b4939w3d-TileDB-0eb1eba
Initialized empty Git repository in /nix/store/phrhd49k173kw7bnrldzif84b4939w3d-TileDB-0eb1eba/.git/
remote: Enumerating objects: 695, done.
remote: Counting objects: 100% (695/695), done.
remote: Compressing objects: 100% (634/634), done.
remote: Total 695 (delta 193), reused 214 (delta 47), pack-reused 0
Receiving objects: 100% (695/695), 16.69 MiB | 27.34 MiB/s, done.
Resolving deltas: 100% (193/193), done.
From https://github.com/TileDB-Inc/TileDB
 * branch            ttd/test-missing-include-fix -> FETCH_HEAD
 * [new branch]      ttd/test-missing-include-fix -> origin/ttd/test-missing-include-fix
Switched to a new branch 'fetchgit'
removing `.git'...
building '/nix/store/bygp9ffv7wv35lcw0af6h708ajaqhbwk-tiledb.drv'...
unpacking sources
unpacking source archive /nix/store/phrhd49k173kw7bnrldzif84b4939w3d-TileDB-0eb1eba
source root is TileDB-0eb1eba
patching sources
configuring
fixing cmake files...
cmake flags: -DCMAKE_FIND_PACKAGE_NO_SYSTEM_PACKAGE_REGISTRY=ON -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_BUILD_TYPE=Release -DCMAKE_SKIP_BUILD_RPATH=ON -DBUILD_TESTING=OFF -DCMAKE_INSTALL_LOCALEDIR=/nix/store/kaql813574xa30591b6js7jx06ygx7x0-tiledb/share/locale -DCMAKE_INSTALL_LIBEXECDIR=/nix/store/kaql813574xa30591b6js7jx06ygx7x0-tiledb/libexec -DCMAKE_INSTALL_LIBDIR=/nix/store/kaql813574xa30591b6js7jx06ygx7x0-tiledb/lib -DCMAKE_INSTALL_DOCDIR=/nix/store/kaql813574xa30591b6js7jx06ygx7x0-tiledb/share/doc/ -DCMAKE_INSTALL_INFODIR=/nix/store/kaql813574xa30591b6js7jx06ygx7x0-tiledb/share/info -DCMAKE_INSTALL_MANDIR=/nix/store/kaql813574xa30591b6js7jx06ygx7x0-tiledb/share/man -DCMAKE_INSTALL_OLDINCLUDEDIR=/nix/store/kaql813574xa30591b6js7jx06ygx7x0-tiledb/include -DCMAKE_INSTALL_INCLUDEDIR=/nix/store/kaql813574xa30591b6js7jx06ygx7x0-tiledb/include -DCMAKE_INSTALL_SBINDIR=/nix/store/kaql813574xa30591b6js7jx06ygx7x0-tiledb/sbin -DCMAKE_INSTALL_BINDIR=/nix/store/kaql813574xa30591b6js7jx06ygx7x0-tiledb/bin -DCMAKE_INSTALL_NAME_DIR=/nix/store/kaql813574xa30591b6js7jx06ygx7x0-tiledb/lib -DCMAKE_POLICY_DEFAULT_CMP0025=NEW -DCMAKE_OSX_DEPLOYMENT_TARGET= -DCMAKE_OSX_SYSROOT= -DCMAKE_FIND_FRAMEWORK=last -DCMAKE_STRIP=/nix/store/mgdjnsrkqgmxqjaqaxgqyqm7fwyi96fk-binutils-2.31.1/bin/strip -DCMAKE_RANLIB=/nix/store/mgdjnsrkqgmxqjaqaxgqyqm7fwyi96fk-binutils-2.31.1/bin/ranlib -DCMAKE_AR=/nix/store/mgdjnsrkqgmxqjaqaxgqyqm7fwyi96fk-binutils-2.31.1/bin/ar -DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=g++ -DCMAKE_INSTALL_PREFIX=/nix/store/kaql813574xa30591b6js7jx06ygx7x0-tiledb
-- The C compiler identification is GNU 7.4.0
-- The CXX compiler identification is GNU 7.4.0
-- Check for working C compiler: /nix/store/hpzj855nkgjvg58nrhq4910sb9q3kss1-gcc-wrapper-7.4.0/bin/gcc
-- Check for working C compiler: /nix/store/hpzj855nkgjvg58nrhq4910sb9q3kss1-gcc-wrapper-7.4.0/bin/gcc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /nix/store/hpzj855nkgjvg58nrhq4910sb9q3kss1-gcc-wrapper-7.4.0/bin/g++
-- Check for working CXX compiler: /nix/store/hpzj855nkgjvg58nrhq4910sb9q3kss1-gcc-wrapper-7.4.0/bin/g++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Starting TileDB superbuild.
-- Found Bzip2: /nix/store/g8al6vdf21mgfi5774qx6r6cil1j7zr8-bzip2-1.0.6.0.1/lib/libbz2.so
-- Found LZ4: /nix/store/6s41b1kn253k4b8dwlyai76d1cazxcdm-lz4-1.9.1/lib/liblz4.so
-- Found Spdlog: /nix/store/3yw2kclpsx02b9hx6ssbbrwlixf5pdi5-spdlog-0.17.0/include
-- Found Zlib: /nix/store/w3wqang215is14xqajycbxmd52b44qkw-zlib-1.2.11/lib/libz.so
-- Found Zstd: /nix/store/aydp0jd0yvg5r5ynsqv1b6i67w736afv-zstd-1.4.1/lib/libzstd.so
-- Found OpenSSL: /nix/store/1g9n3mxrawawa5p9mv8g2baaxjvdg2ag-openssl-1.0.2s/lib/libssl.so /nix/store/1g9n3mxrawawa5p9mv8g2baaxjvdg2ag-openssl-1.0.2s/lib/libcrypto.so
-- Found TBB: /nix/store/g7p34bn41bzmjfi1kabkks8md9bdjx1p-tbb-2019_U8/lib/libtbb.so
-- Found TBB imported target: TBB::tbb
-- searching for catch in /build/TileDB-0eb1eba/build/externals/src
-- Found Catch: /build/TileDB-0eb1eba/build/externals/src/ep_catch/single_include
-- Not found clang-tidy
-- Not found clang-format
-- Found Doxygen: /nix/store/4b4pxa2l331s2z1qd3wh50a30nw22swn-doxygen-1.8.15/bin/doxygen (found version "1.8.15") found components:  doxygen missing components:  dot
-- Install prefix is /nix/store/kaql813574xa30591b6js7jx06ygx7x0-tiledb
-- Configuring done
-- Generating done
CMake Warning:
  Manually-specified variables were not used by the project:

    BUILD_TESTING
    CMAKE_EXPORT_NO_PACKAGE_REGISTRY
    CMAKE_POLICY_DEFAULT_CMP0025


-- Build files have been written to: /build/TileDB-0eb1eba/build
cmake: enabled parallel building
building
build flags: -j8 -l8 SHELL=/nix/store/xfghy8ixrhz3kyy6p724iv3cxji088dx-bash-4.4-p23/bin/bash
Scanning dependencies of target tiledb
[ 12%] Creating directories for 'tiledb'
[ 25%] No download step for 'tiledb'
[ 37%] No update step for 'tiledb'
[ 50%] No patch step for 'tiledb'
[ 62%] Performing configure step for 'tiledb'
-- The C compiler identification is GNU 7.4.0
-- The CXX compiler identification is GNU 7.4.0
-- Check for working C compiler: /nix/store/hpzj855nkgjvg58nrhq4910sb9q3kss1-gcc-wrapper-7.4.0/bin/gcc
-- Check for working C compiler: /nix/store/hpzj855nkgjvg58nrhq4910sb9q3kss1-gcc-wrapper-7.4.0/bin/gcc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /nix/store/hpzj855nkgjvg58nrhq4910sb9q3kss1-gcc-wrapper-7.4.0/bin/g++
-- Check for working CXX compiler: /nix/store/hpzj855nkgjvg58nrhq4910sb9q3kss1-gcc-wrapper-7.4.0/bin/g++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Starting TileDB regular build.
-- The TileDB library is compiled with stats enabled.
-- Found OpenSSL: /nix/store/1g9n3mxrawawa5p9mv8g2baaxjvdg2ag-openssl-1.0.2s/lib/libssl.so /nix/store/1g9n3mxrawawa5p9mv8g2baaxjvdg2ag-openssl-1.0.2s/lib/libcrypto.so
-- Found TBB: /nix/store/g7p34bn41bzmjfi1kabkks8md9bdjx1p-tbb-2019_U8/lib/libtbb.so
-- Found TBB imported target: TBB::tbb
-- Found Bzip2: /nix/store/g8al6vdf21mgfi5774qx6r6cil1j7zr8-bzip2-1.0.6.0.1/lib/libbz2.so
-- Found LZ4: /nix/store/6s41b1kn253k4b8dwlyai76d1cazxcdm-lz4-1.9.1/lib/liblz4.so
-- Found Spdlog: /nix/store/3yw2kclpsx02b9hx6ssbbrwlixf5pdi5-spdlog-0.17.0/include
-- Found Zlib: /nix/store/w3wqang215is14xqajycbxmd52b44qkw-zlib-1.2.11/lib/libz.so
-- Found Zstd: /nix/store/aydp0jd0yvg5r5ynsqv1b6i67w736afv-zstd-1.4.1/lib/libzstd.so
-- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY
-- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY - Success
-- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY
-- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY - Success
-- Performing Test COMPILER_HAS_DEPRECATED_ATTR
-- Performing Test COMPILER_HAS_DEPRECATED_ATTR - Success
-- searching for catch in /build/TileDB-0eb1eba/build/externals/src
-- Found Catch: /build/TileDB-0eb1eba/build/externals/src/ep_catch/single_include
-- Configuring done
-- Generating done
-- Build files have been written to: /build/TileDB-0eb1eba/build/tiledb
[ 75%] Performing build step for 'tiledb'
Scanning dependencies of target TILEDB_CORE_OBJECTS
[  0%] Building CXX object tiledb/CMakeFiles/TILEDB_CORE_OBJECTS.dir/sm/array_schema/domain.cc.o
[  0%] Building CXX object tiledb/CMakeFiles/TILEDB_CORE_OBJECTS.dir/sm/array/array.cc.o
[  3%] Building CXX object tiledb/CMakeFiles/TILEDB_CORE_OBJECTS.dir/sm/array_schema/attribute.cc.o
[  3%] Building CXX object tiledb/CMakeFiles/TILEDB_CORE_OBJECTS.dir/sm/array_schema/array_schema.cc.o
[  3%] Building CXX object tiledb/CMakeFiles/TILEDB_CORE_OBJECTS.dir/sm/array_schema/dimension.cc.o
[  6%] Building CXX object tiledb/CMakeFiles/TILEDB_CORE_OBJECTS.dir/sm/buffer/buffer.cc.o
[  6%] Building CXX object tiledb/CMakeFiles/TILEDB_CORE_OBJECTS.dir/sm/buffer/buffer_list.cc.o
[  6%] Building CXX object tiledb/CMakeFiles/TILEDB_CORE_OBJECTS.dir/sm/buffer/const_buffer.cc.o
[  9%] Building CXX object tiledb/CMakeFiles/TILEDB_CORE_OBJECTS.dir/sm/buffer/preallocated_buffer.cc.o
[  9%] Building CXX object tiledb/CMakeFiles/TILEDB_CORE_OBJECTS.dir/sm/c_api/tiledb.cc.o
[ 12%] Building CXX object tiledb/CMakeFiles/TILEDB_CORE_OBJECTS.dir/sm/cache/lru_cache.cc.o
[ 12%] Building CXX object tiledb/CMakeFiles/TILEDB_CORE_OBJECTS.dir/sm/compressors/bzip_compressor.cc.o
[ 12%] Building CXX object tiledb/CMakeFiles/TILEDB_CORE_OBJECTS.dir/sm/compressors/dd_compressor.cc.o
[ 15%] Building CXX object tiledb/CMakeFiles/TILEDB_CORE_OBJECTS.dir/sm/compressors/gzip_compressor.cc.o
[ 15%] Building CXX object tiledb/CMakeFiles/TILEDB_CORE_OBJECTS.dir/sm/compressors/lz4_compressor.cc.o
[ 15%] Building CXX object tiledb/CMakeFiles/TILEDB_CORE_OBJECTS.dir/sm/compressors/rle_compressor.cc.o
[ 18%] Building CXX object tiledb/CMakeFiles/TILEDB_CORE_OBJECTS.dir/sm/compressors/zstd_compressor.cc.o
[ 18%] Building CXX object tiledb/CMakeFiles/TILEDB_CORE_OBJECTS.dir/sm/encryption/encryption.cc.o
[ 21%] Building CXX object tiledb/CMakeFiles/TILEDB_CORE_OBJECTS.dir/sm/encryption/encryption_key.cc.o
[ 21%] Building CXX object tiledb/CMakeFiles/TILEDB_CORE_OBJECTS.dir/sm/encryption/encryption_key_validation.cc.o
[ 21%] Building CXX object tiledb/CMakeFiles/TILEDB_CORE_OBJECTS.dir/sm/encryption/encryption_openssl.cc.o
[ 24%] Building CXX object tiledb/CMakeFiles/TILEDB_CORE_OBJECTS.dir/sm/encryption/encryption_win32.cc.o
[ 24%] Building CXX object tiledb/CMakeFiles/TILEDB_CORE_OBJECTS.dir/sm/filesystem/hdfs_filesystem.cc.o
[ 24%] Building CXX object tiledb/CMakeFiles/TILEDB_CORE_OBJECTS.dir/sm/filesystem/posix.cc.o
[ 27%] Building CXX object tiledb/CMakeFiles/TILEDB_CORE_OBJECTS.dir/sm/filesystem/s3.cc.o
[ 27%] Building CXX object tiledb/CMakeFiles/TILEDB_CORE_OBJECTS.dir/sm/filesystem/s3_thread_pool_executor.cc.o
[ 30%] Building CXX object tiledb/CMakeFiles/TILEDB_CORE_OBJECTS.dir/sm/filesystem/vfs.cc.o
[ 30%] Building CXX object tiledb/CMakeFiles/TILEDB_CORE_OBJECTS.dir/sm/filesystem/vfs_file_handle.cc.o
[ 30%] Building CXX object tiledb/CMakeFiles/TILEDB_CORE_OBJECTS.dir/sm/filesystem/win.cc.o
[ 33%] Building CXX object tiledb/CMakeFiles/TILEDB_CORE_OBJECTS.dir/sm/filter/bit_width_reduction_filter.cc.o
[ 33%] Building CXX object tiledb/CMakeFiles/TILEDB_CORE_OBJECTS.dir/sm/filter/bitshuffle_filter.cc.o
[ 33%] Building CXX object tiledb/CMakeFiles/TILEDB_CORE_OBJECTS.dir/sm/filter/byteshuffle_filter.cc.o
[ 36%] Building CXX object tiledb/CMakeFiles/TILEDB_CORE_OBJECTS.dir/sm/filter/compression_filter.cc.o
[ 36%] Building CXX object tiledb/CMakeFiles/TILEDB_CORE_OBJECTS.dir/sm/filter/encryption_aes256gcm_filter.cc.o
[ 39%] Building CXX object tiledb/CMakeFiles/TILEDB_CORE_OBJECTS.dir/sm/filter/filter.cc.o
[ 39%] Building CXX object tiledb/CMakeFiles/TILEDB_CORE_OBJECTS.dir/sm/filter/filter_buffer.cc.o
[ 39%] Building CXX object tiledb/CMakeFiles/TILEDB_CORE_OBJECTS.dir/sm/filter/filter_pipeline.cc.o
[ 42%] Building CXX object tiledb/CMakeFiles/TILEDB_CORE_OBJECTS.dir/sm/filter/filter_storage.cc.o
[ 42%] Building CXX object tiledb/CMakeFiles/TILEDB_CORE_OBJECTS.dir/sm/filter/noop_filter.cc.o
[ 42%] Building CXX object tiledb/CMakeFiles/TILEDB_CORE_OBJECTS.dir/sm/filter/positive_delta_filter.cc.o
[ 45%] Building CXX object tiledb/CMakeFiles/TILEDB_CORE_OBJECTS.dir/sm/fragment/fragment_metadata.cc.o
[ 45%] Building CXX object tiledb/CMakeFiles/TILEDB_CORE_OBJECTS.dir/sm/global_state/global_state.cc.o
[ 48%] Building CXX object tiledb/CMakeFiles/TILEDB_CORE_OBJECTS.dir/sm/global_state/libcurl_state.cc.o
[ 48%] Building CXX object tiledb/CMakeFiles/TILEDB_CORE_OBJECTS.dir/sm/global_state/openssl_state.cc.o
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[ 51%] Building CXX object tiledb/CMakeFiles/TILEDB_CORE_OBJECTS.dir/sm/global_state/watchdog.cc.o
[ 51%] Building CXX object tiledb/CMakeFiles/TILEDB_CORE_OBJECTS.dir/sm/kv/kv.cc.o
[ 54%] Building CXX object tiledb/CMakeFiles/TILEDB_CORE_OBJECTS.dir/sm/kv/kv_item.cc.o
[ 54%] Building CXX object tiledb/CMakeFiles/TILEDB_CORE_OBJECTS.dir/sm/kv/kv_iter.cc.o
[ 57%] Building CXX object tiledb/CMakeFiles/TILEDB_CORE_OBJECTS.dir/sm/misc/cancelable_tasks.cc.o
[ 57%] Building CXX object tiledb/CMakeFiles/TILEDB_CORE_OBJECTS.dir/sm/misc/constants.cc.o
[ 57%] Building CXX object tiledb/CMakeFiles/TILEDB_CORE_OBJECTS.dir/sm/misc/logger.cc.o
[ 60%] Building CXX object tiledb/CMakeFiles/TILEDB_CORE_OBJECTS.dir/sm/misc/stats.cc.o
[ 60%] Building CXX object tiledb/CMakeFiles/TILEDB_CORE_OBJECTS.dir/sm/misc/status.cc.o
[ 60%] Building CXX object tiledb/CMakeFiles/TILEDB_CORE_OBJECTS.dir/sm/misc/thread_pool.cc.o
[ 63%] Building CXX object tiledb/CMakeFiles/TILEDB_CORE_OBJECTS.dir/sm/misc/uri.cc.o
[ 63%] Building CXX object tiledb/CMakeFiles/TILEDB_CORE_OBJECTS.dir/sm/misc/utils.cc.o
[ 66%] Building CXX object tiledb/CMakeFiles/TILEDB_CORE_OBJECTS.dir/sm/misc/uuid.cc.o
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[ 75%] Building CXX object tiledb/CMakeFiles/TILEDB_CORE_OBJECTS.dir/sm/serialization/array_schema.cc.o
[ 78%] Building CXX object tiledb/CMakeFiles/TILEDB_CORE_OBJECTS.dir/sm/serialization/query.cc.o
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[ 87%] Building CXX object tiledb/CMakeFiles/TILEDB_CORE_OBJECTS.dir/sm/tile/tile.cc.o
[ 90%] Building CXX object tiledb/CMakeFiles/TILEDB_CORE_OBJECTS.dir/sm/tile/tile_io.cc.o
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[ 96%] Building CXX object tiledb/CMakeFiles/TILEDB_CORE_OBJECTS.dir/__/external/src/blosc/shuffle-sse2.cc.o
[ 96%] Built target TILEDB_CORE_OBJECTS
Scanning dependencies of target tiledb_shared
[100%] Linking CXX shared library libtiledb.so
[100%] Built target tiledb_shared
[ 87%] No install step for 'tiledb'
[100%] Completed 'tiledb'
[100%] Built target tiledb
installing
Scanning dependencies of target doc
[ 50%] Preparing for Doxygen documentation
[100%] Generating API documentation with Doxygen
[100%] Built target doc
Scanning dependencies of target check
[ 53%] Built target TILEDB_CORE_OBJECTS
Scanning dependencies of target tiledb_unit
[ 53%] Building CXX object test/CMakeFiles/tiledb_unit.dir/src/helpers.cc.o
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[ 60%] Building CXX object test/CMakeFiles/tiledb_unit.dir/src/unit-capi-config.cc.o
[ 60%] Building CXX object test/CMakeFiles/tiledb_unit.dir/src/unit-capi-consolidation.cc.o
[ 60%] Building CXX object test/CMakeFiles/tiledb_unit.dir/src/unit-capi-dense_array.cc.o
[ 61%] Building CXX object test/CMakeFiles/tiledb_unit.dir/src/unit-capi-dense_array_2.cc.o
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[ 63%] Building CXX object test/CMakeFiles/tiledb_unit.dir/src/unit-capi-enum_values.cc.o
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[ 65%] Building CXX object test/CMakeFiles/tiledb_unit.dir/src/unit-capi-filter.cc.o
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[ 70%] Building CXX object test/CMakeFiles/tiledb_unit.dir/src/unit-capi-sparse_real.cc.o
[ 71%] Building CXX object test/CMakeFiles/tiledb_unit.dir/src/unit-capi-stats.cc.o
[ 71%] Building CXX object test/CMakeFiles/tiledb_unit.dir/src/unit-capi-sparse_real_2.cc.o
[ 71%] Building CXX object test/CMakeFiles/tiledb_unit.dir/src/unit-capi-string.cc.o
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[ 78%] Building CXX object test/CMakeFiles/tiledb_unit.dir/src/unit-filter-pipeline.cc.o
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[ 81%] Building CXX object test/CMakeFiles/tiledb_unit.dir/src/unit-s3-no-multipart.cc.o
[ 83%] Building CXX object test/CMakeFiles/tiledb_unit.dir/src/unit-status.cc.o
[ 83%] Building CXX object test/CMakeFiles/tiledb_unit.dir/src/unit-Consolidator.cc.o
[ 85%] Building CXX object test/CMakeFiles/tiledb_unit.dir/src/unit-Subarray.cc.o
[ 85%] Building CXX object test/CMakeFiles/tiledb_unit.dir/src/unit-SubarrayPartitioner-dense.cc.o
[ 85%] Building CXX object test/CMakeFiles/tiledb_unit.dir/src/unit-SubarrayPartitioner-error.cc.o
[ 86%] Building CXX object test/CMakeFiles/tiledb_unit.dir/src/unit-SubarrayPartitioner-sparse.cc.o
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[ 95%] Building CXX object test/CMakeFiles/tiledb_unit.dir/src/unit-cppapi-schema.cc.o
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[ 98%] Building CXX object test/CMakeFiles/tiledb_unit.dir/src/unit-cppapi-vfs.cc.o
[100%] Linking CXX executable tiledb_unit
[100%] Built target tiledb_unit
Scanning dependencies of target check
UpdateCTestConfiguration  from :/build/TileDB-0eb1eba/build/tiledb/test/DartConfiguration.tcl
UpdateCTestConfiguration  from :/build/TileDB-0eb1eba/build/tiledb/test/DartConfiguration.tcl
Test project /build/TileDB-0eb1eba/build/tiledb/test
Constructing a list of tests
Done constructing a list of tests
Updating test list for fixtures
Added 0 tests to meet fixture requirements
Checking test dependency graph...
Checking test dependency graph end
test 1
    Start 1: tiledb_unit

1: Test command: /build/TileDB-0eb1eba/build/tiledb/test/tiledb_unit "--durations=yes"
1: Test timeout computed to be: 10000000
1: 0.002 s: Backwards compatibility: Test error opening 1.3.0 array
1: 0.002 s: Backwards compatibility: Test reading 1.4.0 array with non-split coords
1: 0.001 s: Backwards compatibility: Test reading arrays written with previous version of tiledb
1: 0.001 s: Backwards compatibility: Write to an array of older version
1: 0.000 s: Buffer: Test default constructor with write void*
1: 0.000 s: Buffer: Test swap
1: 0.000 s: Buffer: Test move
1: 0.000 s: BufferList: Test append
1: 0.000 s: BufferList: Test read
1: 0.001 s: C API: Test empty BufferList
1: 0.001 s: C API: Test BufferList get buffers
1: 0.013 s: C API: Test `ANY` datatype
1: 0.000 s: - No serialization
1: 0.006 s: C API: Test array schema creation and retrieval
1: 0.000 s: - Serialization
1: 0.006 s: C API: Test array schema creation and retrieval
1: 0.002 s: C API: Test array schema one anonymous dimension
1: 0.002 s: C API: Test array schema multiple anonymous dimensions
1: 0.002 s: C API: Test array schema one anonymous attribute
1: 0.002 s: C API: Test array schema multiple anonymous attributes
1: 0.002 s: C API: Test array schema with invalid float dense domain
1: 0.002 s: C API: Test array schema with invalid dimension domain and tile extent
1: 0.002 s: C API: Test NAN and INF in dimensions
1: 0.000 s: - No serialization
1: 0.004 s: C API: Test array schema offsets/coords filter lists
1: 0.000 s: - Serialization
1: 0.004 s: C API: Test array schema offsets/coords filter lists
1: 0.000 s: - No serialization
1: 0.006 s: C API: Test array schema load error condition
1: 0.000 s: - Serialization
1: 0.006 s: C API: Test array schema load error condition
1: 0.013 s: C API: Test dense async
1: 0.015 s: C API: Test sparse async
1: 0.014 s: C API: Test async cancellation
1: 0.004 s: C API: Test getting array URI
1: 0.002 s: C API: Set null URI
1: 0.003 s: - API calls with encrypted schema
1: 0.005 s: C API: Test array with encryption
1: 0.002 s: - API calls with unencrypted schema
1: 0.004 s: C API: Test array with encryption
1: 0.000 s: - without encryption
1: 0.014 s: C API: Test opening array at timestamp
1: 0.000 s: - with encryption
1: 0.015 s: C API: Test opening array at timestamp
1: 0.002 s: ### dense
1: 0.002 s: ** 1D
1: 0.002 s: - Check out-of-bounds coordinates
1: 0.006 s: C API: Check writing coordinates out of bounds
1: 0.002 s: ### sparse
1: 0.002 s: ** 1D
1: 0.002 s: - Check out-of-bounds coordinates
1: 0.007 s: C API: Check writing coordinates out of bounds
1: 0.002 s: ### dense
1: 0.002 s: ** 2D
1: 0.002 s: - Check out-of-bounds coordinates
1: 0.006 s: C API: Check writing coordinates out of bounds
1: 0.002 s: ### sparse
1: 0.002 s: ** 2D
1: 0.002 s: - Check out-of-bounds coordinates
1: 0.005 s: C API: Check writing coordinates out of bounds
1: 0.002 s: ### dense
1: 0.002 s: ** 1D
1: 0.002 s: - Do not check out-of-bounds coordinates
1: 0.011 s: C API: Check writing coordinates out of bounds
1: 0.002 s: ### sparse
1: 0.002 s: ** 1D
1: 0.002 s: - Do not check out-of-bounds coordinates
1: 0.011 s: C API: Check writing coordinates out of bounds
1: 0.002 s: ### dense
1: 0.002 s: ** 2D
1: 0.002 s: - Do not check out-of-bounds coordinates
1: 0.011 s: C API: Check writing coordinates out of bounds
1: 0.002 s: ### sparse
1: 0.002 s: ** 2D
1: 0.002 s: - Do not check out-of-bounds coordinates
1: 0.011 s: C API: Check writing coordinates out of bounds
1: 0.004 s: C API: Test empty array
1: 0.010 s: C API: Test array with no filelocks
1: 0.000 s: - Check size and data pointer
1: 0.001 s: C API: Test buffer
1: 0.000 s: - Check get/set datatype
1: 0.001 s: C API: Test buffer
1: 0.000 s: - Check get/set buffer
1: 0.001 s: C API: Test buffer
1: 0.003 s: C API: Test config
1: 0.001 s: C API: Test config iter
1: 0.007 s: C API: Test config from file
1: 0.000 s: C API: Test boolean config values are normalized
1: 0.040 s: - write full, subarray, unordered
1: 0.044 s: C API: Test consolidation, dense
1: 0.042 s: - write subarray, full, unordered
1: 0.045 s: C API: Test consolidation, dense
1: 0.029 s: - write subarray, unordered, full
1: 0.033 s: C API: Test consolidation, dense
1: 0.034 s: - write (encrypted) subarray, unordered, full
1: 0.038 s: C API: Test consolidation, dense
1: 0.036 s: - write full, unordered
1: 0.039 s: C API: Test consolidation, sparse
1: 0.035 s: - write unordered, full
1: 0.039 s: C API: Test consolidation, sparse
1: 0.038 s: - write (encrypted) unordered, full
1: 0.041 s: C API: Test consolidation, sparse
1: 0.028 s: - write key A,B,C; A,C,D
1: 0.032 s: C API: Test consolidation, KV
1: 0.029 s: - write keys A,C,D; A,B,C
1: 0.032 s: C API: Test consolidation, KV
1: 0.033 s: - write (encrypted) keys A,C,D; A,B,C
1: 0.036 s: C API: Test consolidation, KV
1: 0.020 s: C API: Test advanced consolidation, wrong configs
1: 0.026 s: C API: Test advanced consolidation #1
1: 0.031 s: C API: Test advanced consolidation #2
1: 0.021 s: C API: Test advanced consolidation #3
1: 0.025 s: C API: Test advanced consolidation #4
1: 0.030 s: C API: Test advanced consolidation #5
1: 0.036 s: C API: Test advanced consolidation #6
1: 0.026 s: C API: Test advanced consolidation #7
1: 0.026 s: C API: Test advanced consolidation #8
1: 0.027 s: C API: Test consolidation, fragments that don't coincide with space tiles #1
1: 0.026 s: C API: Test consolidation, fragments that don't coincide with space tiles #2
1: 0.052 s: C API: Test advanced consolidation, small buffer size
1: 0.031 s: C API: Test advanced consolidation, encrypted array
1: 0.031 s: C API: Test advanced consolidation, dense array mixing both sparse and dense fragments
1: 0.022 s: C API: Test advanced consolidation, overwritten fragments, no deletion
1: 0.031 s: C API: Test advanced consolidation, overwritten fragments, deletion #1
1: 0.025 s: C API: Test advanced consolidation, overwritten fragments, deletion #2
1: 0.030 s: C API: Test advanced consolidation, overwritten fragments, deletion #3
1: 0.018 s: C API: Test advanced consolidation, consolidatable #1
1: 0.000 s: - should consolidate
1: 0.018 s: C API: Test advanced consolidation, consolidatable #2
1: 0.000 s: - should not consolidate
1: 0.014 s: C API: Test advanced consolidation, consolidatable #2
1: 0.000 s: - No serialization
1: 1.799 s: C API: Test dense array, sorted reads
1: 0.000 s: - Serialization
1: 1.652 s: C API: Test dense array, sorted reads
1: 0.000 s: - No serialization
1: 0.007 s: C API: Test dense array, invalid number of cells in dense writes
1: 0.000 s: - Serialization
1: 0.006 s: C API: Test dense array, invalid number of cells in dense writes
1: 0.000 s: - No serialization
1: 0.056 s: C API: Test dense array, sorted writes
1: 0.000 s: - Serialization
1: 0.054 s: C API: Test dense array, sorted writes
1: 0.000 s: - No serialization
1: 0.024 s: C API: Test dense array, sparse writes
1: 0.000 s: - Serialization
1: 0.023 s: C API: Test dense array, sparse writes
1: 0.000 s: - No serialization
1: 0.085 s: C API: Test dense array, simultaneous writes
1: 0.000 s: - Serialization
1: 0.084 s: C API: Test dense array, simultaneous writes
1: 0.000 s: - No serialization
1: 0.040 s: C API: Test dense array, cancel and retry writes
1: 0.000 s: - Serialization
1: 0.041 s: C API: Test dense array, cancel and retry writes
1: 0.000 s: - No serialization
1: 0.017 s: C API: Test dense array, return coordinates
1: 0.000 s: - Serialization
1: 0.017 s: C API: Test dense array, return coordinates
1: 0.000 s: - No serialization
1: 0.014 s: C API: Test dense array, non-empty domain
1: 0.000 s: - Serialization
1: 0.014 s: C API: Test dense array, non-empty domain
1: 0.000 s: - No serialization
1: 0.014 s: C API: Test dense array, invalid set query buffer
1: 0.000 s: - Serialization
1: 0.013 s: C API: Test dense array, invalid set query buffer
1: 0.004 s: C API: Test dense array, open array checks
1: 0.023 s: C API: Test dense array, reopen array checks
1: 0.000 s: - No serialization
1: 0.013 s: C API: Test dense array, reset read subarray
1: 0.000 s: - Serialization
1: 0.013 s: C API: Test dense array, reset read subarray
1: 0.000 s: - No serialization
1: 0.020 s: C API: Test dense array, reset write subarray
1: 0.000 s: - Serialization
1: 0.019 s: C API: Test dense array, reset write subarray
1: 0.000 s: - No serialization
1: 0.014 s: C API: Test dense array, URI ending in a slash
1: 0.000 s: - Serialization
1: 0.013 s: C API: Test dense array, URI ending in a slash
1: 0.000 s: - No serialization
1: 0.005 s: C API: Test dense array, missing attributes in writes
1: 0.000 s: - Serialization
1: 0.004 s: C API: Test dense array, missing attributes in writes
1: 0.000 s: - No serialization
1: 0.008 s: C API: Test dense array, read subarrays with empty cells
1: 0.000 s: - Serialization
1: 0.008 s: C API: Test dense array, read subarrays with empty cells
1: 0.000 s: - No serialization
1: 0.010 s: C API: Test dense array, read subarrays with empty areas around sparse cells
1: 0.000 s: - Serialization
1: 0.010 s: C API: Test dense array, read subarrays with empty areas around sparse cells
1: 0.000 s: - No serialization
1: 0.008 s: C API: Test dense array, read subarrays with empty areas, merging adjacent cell ranges
1: 0.000 s: - Serialization
1: 0.008 s: C API: Test dense array, read subarrays with empty areas, merging adjacent cell ranges
1: 0.000 s: - No serialization
1: 0.012 s: C API: Test dense array, multi-fragment reads
1: 0.000 s: - Serialization
1: 0.012 s: C API: Test dense array, multi-fragment reads
1: 0.000 s: - No serialization
1: 0.004 s: C API: Test dense array, check if open
1: 0.000 s: - Serialization
1: 0.004 s: C API: Test dense array, check if open
1: 0.000 s: - No serialization
1: 0.004 s: C API: Test dense array, get schema from opened array
1: 0.000 s: - Serialization
1: 0.004 s: C API: Test dense array, get schema from opened array
1: 0.000 s: - No serialization
1: 0.005 s: C API: Test dense array, set subarray in sparse writes should error
1: 0.000 s: - Serialization
1: 0.005 s: C API: Test dense array, set subarray in sparse writes should error
1: 0.000 s: - No serialization
1: 0.015 s: C API: Test dense array, check if coords exist in unordered writes
1: 0.000 s: - Serialization
1: 0.016 s: C API: Test dense array, check if coords exist in unordered writes
1: 0.000 s: - No serialization
1: 0.016 s: C API: Test dense array, read in col-major after updates
1: 0.000 s: - Serialization
1: 0.016 s: C API: Test dense array, read in col-major after updates
1: 1.664 s: C API: Test dense array, encrypted
1: 0.025 s: C API: Test dense vector, mixed dense and sparse fragments
1: 0.014 s: Dense array: 1D, full read
1: 0.024 s: Dense array: 1D, full read, 1 dense fragment, 1 sparse fragment
1: 0.025 s: Dense array: 1D, full read, 1 dense fragment, 1 sparse fragment, sparse overwritten
1: 0.000 s: - subarray: row
1: 0.014 s: Dense array: 2D, full read
1: 0.000 s: - subarray: col
1: 0.015 s: Dense array: 2D, full read
1: 0.000 s: - subarray: global
1: 0.014 s: Dense array: 2D, full read
1: 0.013 s: Dense array: 2D, error, multi-range global reads
1: 0.000 s: - subarray: row
1: 0.024 s: Dense array: 2D, full read, 1 dense fragment, 1 sparse fragment
1: 0.000 s: - subarray: col
1: 0.025 s: Dense array: 2D, full read, 1 dense fragment, 1 sparse fragment
1: 0.000 s: - subarray: global
1: 0.026 s: Dense array: 2D, full read, 1 dense fragment, 1 sparse fragment
1: 0.000 s: - subarray: row
1: 0.025 s: Dense array: 2D, multi-range, 1 dense fragment, 1 sparse fragment
1: 0.000 s: - subarray: col
1: 0.024 s: Dense array: 2D, multi-range, 1 dense fragment, 1 sparse fragment
1: 0.008 s: C API: Test 1d dense vector with negative domain
1: 0.018 s: C API: Test 2d dense array with negative domain
1: 0.040 s: C API: Test 1d dense vector
1: 0.039 s: C API: Test 1d dense vector with anonymous attribute
1: 0.008 s: C API: Test 1d dense vector cell/tile layout
1: 0.019 s: C API: Test 1d dense vector, update
1: 0.000 s: C API: Test enum values
1: 0.000 s: C API: Test enum string conversion
1: 0.001 s: C API: Test error and error message
1: 0.001 s: C API: Test filter set option
1: 0.001 s: C API: Test filter list
1: 0.001 s: C API: Test filter list on attribute
1: 0.014 s: C API: Test incomplete read queries, dense
1: 0.016 s: C API: Test incomplete read queries, sparse
1: 0.013 s: C API: Test incomplete read queries 2, dense
1: 0.016 s: C API: Test incomplete read queries 2, sparse
1: 0.004 s: C API: Test key-value mode
1: 0.053 s: C API: Test key-value write, read and iter
1: 0.056 s: C API: Test encrypted key-value write, read and iter
1: 0.052 s: C API: Test key-value, anonymous attribute
1: 0.004 s: C API: Test key-value, get schema from opened kv
1: 0.000 s: - without encryption
1: 0.015 s: C API: Test opening key-value store at timestamp
1: 0.000 s: - with encryption
1: 0.016 s: C API: Test opening key-value store at timestamp
1: 0.007 s: C API: Test object management methods: object_type, delete, move
1: 0.004 s: C API: Test object management methods: walk, ls
1: 0.002 s: C API: Test listing directory with >1000 objects on S3
1: 0.004 s: C API: Test query get buffer
1: 0.004 s: C API: Test query get layout
1: 0.003 s: C API: Test subarray, sparse, basic API usage and errors
1: 0.003 s: C API: Test subarray, sparse, check default (empty) subarray
1: 0.003 s: C API: Test subarray, sparse, check NaN ranges
1: 0.003 s: C API: Test subarray, sparse, result estimation, empty tree
1: 0.000 s: -- Full overlap
1: 0.011 s: - row-major
1: 0.012 s: C API: Test subarray, sparse, 1D, result estimation, height 2
1: 0.000 s: -- No overlap, 1 range
1: 0.011 s: - row-major
1: 0.012 s: C API: Test subarray, sparse, 1D, result estimation, height 2
1: 0.000 s: -- No overlap, 2 ranges
1: 0.011 s: - row-major
1: 0.012 s: C API: Test subarray, sparse, 1D, result estimation, height 2
1: 0.000 s: -- Partial overlap, 1 range
1: 0.011 s: - row-major
1: 0.012 s: C API: Test subarray, sparse, 1D, result estimation, height 2
1: 0.000 s: -- Partial overlap, 2 ranges
1: 0.011 s: - row-major
1: 0.012 s: C API: Test subarray, sparse, 1D, result estimation, height 2
1: 0.000 s: -- Full overlap
1: 0.010 s: - col-major
1: 0.012 s: C API: Test subarray, sparse, 1D, result estimation, height 2
1: 0.000 s: -- No overlap, 1 range
1: 0.011 s: - col-major
1: 0.012 s: C API: Test subarray, sparse, 1D, result estimation, height 2
1: 0.000 s: -- No overlap, 2 ranges
1: 0.010 s: - col-major
1: 0.012 s: C API: Test subarray, sparse, 1D, result estimation, height 2
1: 0.000 s: -- Partial overlap, 1 range
1: 0.011 s: - col-major
1: 0.012 s: C API: Test subarray, sparse, 1D, result estimation, height 2
1: 0.000 s: -- Partial overlap, 2 ranges
1: 0.011 s: - col-major
1: 0.012 s: C API: Test subarray, sparse, 1D, result estimation, height 2
1: 0.000 s: -- Full overlap
1: 0.011 s: - row-major
1: 0.012 s: C API: Test subarray, sparse, 1D, result estimation, height 3
1: 0.000 s: -- No overlap, 1 range
1: 0.011 s: - row-major
1: 0.012 s: C API: Test subarray, sparse, 1D, result estimation, height 3
1: 0.000 s: -- No overlap, 2 ranges
1: 0.011 s: - row-major
1: 0.012 s: C API: Test subarray, sparse, 1D, result estimation, height 3
1: 0.000 s: -- Overlap only tiles, 1 range
1: 0.011 s: - row-major
1: 0.012 s: C API: Test subarray, sparse, 1D, result estimation, height 3
1: 0.000 s: -- Overlap only tiles, 2 ranges
1: 0.011 s: - row-major
1: 0.012 s: C API: Test subarray, sparse, 1D, result estimation, height 3
1: 0.000 s: -- Overlap only tile ranges, 1 range
1: 0.011 s: - row-major
1: 0.012 s: C API: Test subarray, sparse, 1D, result estimation, height 3
1: 0.000 s: -- Overlap only tile ranges, 2 ranges
1: 0.011 s: - row-major
1: 0.012 s: C API: Test subarray, sparse, 1D, result estimation, height 3
1: 0.000 s: -- Overlap tiles and tile ranges
1: 0.011 s: - row-major
1: 0.012 s: C API: Test subarray, sparse, 1D, result estimation, height 3
1: 0.000 s: -- Full overlap
1: 0.011 s: - col-major
1: 0.012 s: C API: Test subarray, sparse, 1D, result estimation, height 3
1: 0.000 s: -- No overlap, 1 range
1: 0.011 s: - col-major
1: 0.012 s: C API: Test subarray, sparse, 1D, result estimation, height 3
1: 0.000 s: -- No overlap, 2 ranges
1: 0.011 s: - col-major
1: 0.013 s: C API: Test subarray, sparse, 1D, result estimation, height 3
1: 0.000 s: -- Overlap only tiles, 1 range
1: 0.011 s: - col-major
1: 0.013 s: C API: Test subarray, sparse, 1D, result estimation, height 3
1: 0.000 s: -- Overlap only tiles, 2 ranges
1: 0.011 s: - col-major
1: 0.013 s: C API: Test subarray, sparse, 1D, result estimation, height 3
1: 0.000 s: -- Overlap only tile ranges, 1 range
1: 0.011 s: - col-major
1: 0.012 s: C API: Test subarray, sparse, 1D, result estimation, height 3
1: 0.000 s: -- Overlap only tile ranges, 2 ranges
1: 0.011 s: - col-major
1: 0.012 s: C API: Test subarray, sparse, 1D, result estimation, height 3
1: 0.000 s: -- Overlap tiles and tile ranges
1: 0.011 s: - col-major
1: 0.012 s: C API: Test subarray, sparse, 1D, result estimation, height 3
1: 0.000 s: -- Full overlap
1: 0.012 s: - row-major
1: 0.013 s: C API: Test subarray, sparse, 2D, result estimation, height 2
1: 0.000 s: -- No overlap, 1 range
1: 0.011 s: - row-major
1: 0.012 s: C API: Test subarray, sparse, 2D, result estimation, height 2
1: 0.000 s: -- No overlap, 4 ranges
1: 0.012 s: - row-major
1: 0.013 s: C API: Test subarray, sparse, 2D, result estimation, height 2
1: 0.000 s: -- Partial overlap, 1 range
1: 0.012 s: - row-major
1: 0.013 s: C API: Test subarray, sparse, 2D, result estimation, height 2
1: 0.000 s: -- Partial overlap, 4 ranges
1: 0.011 s: - row-major
1: 0.012 s: C API: Test subarray, sparse, 2D, result estimation, height 2
1: 0.000 s: -- Full overlap
1: 0.011 s: - col-major
1: 0.012 s: C API: Test subarray, sparse, 2D, result estimation, height 2
1: 0.000 s: -- No overlap, 1 range
1: 0.011 s: - col-major
1: 0.012 s: C API: Test subarray, sparse, 2D, result estimation, height 2
1: 0.000 s: -- No overlap, 4 ranges
1: 0.011 s: - col-major
1: 0.012 s: C API: Test subarray, sparse, 2D, result estimation, height 2
1: 0.000 s: -- Partial overlap, 1 range
1: 0.010 s: - col-major
1: 0.012 s: C API: Test subarray, sparse, 2D, result estimation, height 2
1: 0.000 s: -- Partial overlap, 4 ranges
1: 0.010 s: - col-major
1: 0.011 s: C API: Test subarray, sparse, 2D, result estimation, height 2
1: 0.003 s: C API: Test subarray, dense, result estimation, empty array
1: 0.010 s: C API: Test subarray, dense, result estimation, 1 range, full tile
1: 0.010 s: C API: Test subarray, dense, result estimation, 1 range, 2 full tiles
1: 0.010 s: C API: Test subarray, dense, result estimation, 1 range, partial tiles
1: 0.010 s: C API: Test subarray, dense, result estimation, multiple ranges
1: 0.010 s: C API: Test subarray, dense, result estimation, non-coinciding domain
1: 0.017 s: C API: Test subarray, dense, result estimation, 1 range, 2 dense frags
1: 0.018 s: C API: Test subarray, dense, result estimation, 1 range, mixed frags
1: 1.561 s: - no compression, row/row-major
1: 1.567 s: C API: Test sparse array, sorted reads
1: 1.555 s: - no compression, col/col-major
1: 1.563 s: C API: Test sparse array, sorted reads
1: 1.456 s: - no compression, row/col-major
1: 1.461 s: C API: Test sparse array, sorted reads
1: 1.814 s: - gzip compression, row/row-major
1: 1.817 s: C API: Test sparse array, sorted reads
1: 1.808 s: - gzip compression, col/col-major
1: 1.811 s: C API: Test sparse array, sorted reads
1: 1.672 s: - gzip compression, row/col-major
1: 1.676 s: C API: Test sparse array, sorted reads
1: 1.854 s: - bzip compression, row/col-major
1: 1.860 s: C API: Test sparse array, sorted reads
1: 1.494 s: - lz4 compression, row/col-major
1: 1.499 s: C API: Test sparse array, sorted reads
1: 1.493 s: - rle compression, row/col-major
1: 1.499 s: C API: Test sparse array, sorted reads
1: 1.460 s: - zstd compression, row/col-major
1: 1.465 s: C API: Test sparse array, sorted reads
1: 1.434 s: - double-delta compression, row/col-major
1: 1.437 s: C API: Test sparse array, sorted reads
1: 0.000 s: - unordered, error check
1: 0.005 s: C API: Test sparse array, duplicates
1: 0.011 s: - unordered, no error check
1: 0.016 s: C API: Test sparse array, duplicates
1: 0.012 s: - unordered, dedup
1: 0.017 s: C API: Test sparse array, duplicates
1: 0.012 s: - unordered, all duplicates, dedup
1: 0.016 s: C API: Test sparse array, duplicates
1: 0.002 s: - global, error check
1: 0.007 s: C API: Test sparse array, duplicates
1: 0.011 s: - global, no error check
1: 0.015 s: C API: Test sparse array, duplicates
1: 0.012 s: - global, dedup
1: 0.017 s: C API: Test sparse array, duplicates
1: 0.012 s: - global, all duplicates, dedup
1: 0.016 s: C API: Test sparse array, duplicates
1: 0.015 s: C API: Test sparse array, non-empty domain
1: 0.004 s: C API: Test sparse array, invalid offsets on write
1: 1.595 s: C API: Test sparse array, anonymous attribute
1: 0.018 s: C API: Test sparse array, no results
1: 0.004 s: C API: Test sparse array, missing attributes in writes
1: 0.005 s: C API: Test sparse array, set subarray should error
1: 0.006 s: C API: Test sparse array, check if coords exist
1: 0.005 s: C API: Test sparse array, global order check on write
1: 0.017 s: C API: Test sparse array, invalidate cached max buffer sizes
1: 1.864 s: C API: Test sparse array, encrypted
1: 0.027 s: C API: Test sparse array, calibrate est size
1: 0.027 s: C API: Test sparse array, calibrate est size, unary
1: 0.029 s: C API: Test sparse array, calibrate est size, huge range
1: 0.016 s: C API: Test sparse array, multi-subarray, 2D, complete
1: 0.016 s: C API: Test sparse array, multi-subarray, 2D, multiplicities
1: 0.016 s: C API: Test sparse array, multi-subarray, 2D, incomplete
1: 0.017 s: C API: Test sparse array, multi-subarray, 2D, complete, col
1: 0.019 s: C API: Test sparse array 2, multi-range subarray, row-major
1: 0.017 s: C API: Test sparse array, multi-range subarray, col-major
1: 0.016 s: C API: Test sparse array, multi-range subarray, row-major, incomplete 1
1: 0.016 s: C API: Test sparse array, multi-range subarray, col-major, incomplete 1
1: 0.017 s: C API: Test sparse array, multi-range subarray, row-major, incomplete 2
1: 0.017 s: C API: Test sparse array, multi-range subarray, col-major, incomplete 2
1: 0.016 s: C API: Test sparse array, multi-range subarray, row-major, incomplete 3
1: 0.018 s: C API: Test sparse array, multi-range subarray, row-major, incomplete 4
1: 0.017 s: C API: Test sparse array, multi-range subarray, col-major, incomplete 4
1: 0.016 s: C API: Test sparse array, multi-range subarray, row-major, incomplete 5
1: 0.016 s: C API: Test sparse array, multi-range subarray, col-major, incomplete 5
1: 0.005 s: C API: Test sparse array, global order with 0-sized buffers
1: 0.010 s: C API: Test 1d sparse vector with negative domain
1: 0.011 s: C API: Test 2d sparse array with negative domain
1: 0.010 s: C API: Test 1d sparse vector with negative domain 2
1: 0.011 s: C API: Test 2d sparse array with negative domain 2
1: 0.010 s: C API: Test 2d sparse array with real domain
1: 0.010 s: C API: Test 2d sparse array with real domain, next subarray partition bug
1: 0.010 s: C API: Test 2d sparse array with real domain, NaN in subarray
1: 0.000 s: C API: Test stats
1: 0.010 s: C API: Test 2d sparse array with real domain 2
1: 0.010 s: C API: Test 2d sparse array with real domain, next subarray partition bug 2
1: 0.010 s: C API: Test 2d sparse array with real domain, NaN in subarray 2
1: 0.016 s: C API: Test 2d sparse array with real domain 2, unary range
1: 0.017 s: C API: Test string support
1: 0.001 s: C API: Test URI
1: 0.000 s: C API: Test version
1: 0.014 s: C API: Test virtual filesystem
1: 0.002 s: C API: Test virtual filesystem when S3 is not supported
1: 0.002 s: C API: Test virtual filesystem config
1: 0.016 s: C API: Test VFS parallel I/O
1: 0.002 s: CellSlabIter: Empty iterator
1: 0.005 s: CellSlabIter: Error checks
1: 0.004 s: CellSlabIter: Test 1D ranges
1: 0.004 s: CellSlabIter: Test 2D ranges
1: 0.004 s: CellSlabIter: Test 1D slabs
1: 0.000 s: - row-major
1: 0.004 s: CellSlabIter: Test 2D slabs
1: 0.000 s: - col-major
1: 0.004 s: CellSlabIter: Test 2D slabs
1: 0.000 s: Compression-DoubleDelta: Test 1-element case
1: 0.000 s: Compression-DoubleDelta: Test 2-element case
1: 0.000 s: Compression-DoubleDelta: Test 3-element case
1: 0.000 s: Compression-DoubleDelta: Test 4-element case
1: 0.054 s: Compression-DoubleDelta: Test n-element case
1: 0.000 s: Compression-DoubleDelta: Test uncompressible case
1: 0.000 s: Compression-RLE: Test invalid format
1: 0.000 s: Compression-RLE: Test all values unique
1: 0.000 s: Compression-RLE: Test all values the same
1: 0.000 s: Compression-RLE: Test a mix of short and long runs
1: 0.001 s: Compression-RLE: Test when a run exceeds max run length
1: 0.000 s: Compression-RLE: Test compression/decompression with type double:2
1: 0.000 s: - Basic
1: 0.000 s: Encryption: Test AES-256-GCM
1: 0.000 s: - Plaintext encrypts differently
1: 0.000 s: Encryption: Test AES-256-GCM
1: 0.001 s: - Different input lengths
1: 0.001 s: Encryption: Test AES-256-GCM
1: 0.000 s: - NIST test vectors
1: 0.000 s: Encryption: Test AES-256-GCM
1: 0.000 s: FilterBuffer: Test init
1: 0.000 s: FilterBuffer: Test prepend
1: 0.000 s: FilterBuffer: Test multiple reads/writes
1: 0.000 s: FilterBuffer: Test write from other
1: 0.000 s: FilterBuffer: Test get ConstBuffer
1: 0.000 s: FilterBuffer: Test clear
1: 0.000 s: FilterBuffer: Test copy_to
1: 0.000 s: FilterBuffer: Test append_view
1: 0.000 s: FilterBuffer: Test view reclaim
1: 0.000 s: - Prepend buffer
1: 0.000 s: FilterBuffer: Test fixed allocation
1: 0.000 s: - Prepend too large buffer
1: 0.000 s: FilterBuffer: Test fixed allocation
1: 0.000 s: - Append view
1: 0.000 s: FilterBuffer: Test fixed allocation
1: 0.000 s: - Append too large view
1: 0.000 s: FilterBuffer: Test fixed allocation
1: 0.000 s: FilterBuffer: Test copy with reinterpret type
1: 0.000 s: FilterBuffer: Test read-only
1: 0.000 s: Filter: Test empty pipeline
1: 0.000 s: - Single stage
1: 0.000 s: Filter: Test simple in-place pipeline
1: 0.000 s: - Multi-stage
1: 0.000 s: Filter: Test simple in-place pipeline
1: 0.000 s: - Single stage
1: 0.000 s: Filter: Test simple out-of-place pipeline
1: 0.000 s: - Multi-stage
1: 0.000 s: Filter: Test simple out-of-place pipeline
1: 0.000 s: Filter: Test mixed in- and out-of-place pipeline
1: 0.000 s: - Simple
1: 0.000 s: Filter: Test compression
1: 0.000 s: - With checksum stage
1: 0.000 s: Filter: Test compression
1: 0.000 s: - With multiple stages
1: 0.000 s: Filter: Test compression
1: 0.000 s: - Single stage
1: 0.000 s: Filter: Test pseudo-checksum
1: 0.000 s: - Multi-stage
1: 0.000 s: Filter: Test pseudo-checksum
1: 0.000 s: Filter: Test pipeline modify filter
1: 0.000 s: Filter: Test pipeline copy
1: 0.274 s: Filter: Test random pipeline
1: 0.000 s: - Single stage
1: 0.000 s: Filter: Test bit width reduction
1: 0.001 s: - Window sizes
1: 0.001 s: Filter: Test bit width reduction
1: 0.000 s: - Random values
1: 0.000 s: Filter: Test bit width reduction
1: 0.000 s:  - Random signed values
1: 0.000 s: Filter: Test bit width reduction
1: 0.000 s: - Byte overflow
1: 0.000 s: Filter: Test bit width reduction
1: 0.000 s: - Single stage
1: 0.000 s: Filter: Test positive-delta encoding
1: 0.001 s: - Window sizes
1: 0.001 s: Filter: Test positive-delta encoding
1: 0.000 s: - Error on non-positive delta data
1: 0.000 s: Filter: Test positive-delta encoding
1: 0.000 s: - Single stage
1: 0.000 s: Filter: Test bitshuffle
1: 0.000 s: - Indivisible by 8
1: 0.000 s: Filter: Test bitshuffle
1: 0.000 s: - Single stage
1: 0.000 s: Filter: Test byteshuffle
1: 0.000 s: - Uneven number of elements
1: 0.000 s: Filter: Test byteshuffle
1: 0.000 s: - AES-256-GCM
1: 0.000 s: Filter: Test encryption
1: 0.000 s: Unit-test class LRUCache
1: 0.000 s: LRUCache item invalidation
1: 0.002 s: Reader: Compute result space tiles, 2D
1: 0.002 s: ResultCellSlabIter: Empty iterator
1: 0.004 s: ResultCellSlabIter: Test 1D slabs, 1 fragment, full overlap
1: 0.005 s: ResultCellSlabIter: Test 1D slabs, 1 fragment, no overlap
1: 0.004 s: ResultCellSlabIter: Test 1D slabs, 2 fragments
1: 0.004 s: ResultCellSlabIter: Test 1D slabs, 1 dense fragment, 2 sparse fragments
1: 0.000 s: - tile: row, cell: row, subarray: row
1: 0.004 s: ResultCellSlabIter: Test 2D slabs, 1 range, 1 dense fragment, full overlap
1: 0.000 s: - tile: row, cell: col, subarray: row
1: 0.004 s: ResultCellSlabIter: Test 2D slabs, 1 range, 1 dense fragment, full overlap
1: 0.000 s: - tile: col, cell: row, subarray: row
1: 0.004 s: ResultCellSlabIter: Test 2D slabs, 1 range, 1 dense fragment, full overlap
1: 0.000 s: - tile: col, cell: col, subarray: row
1: 0.004 s: ResultCellSlabIter: Test 2D slabs, 1 range, 1 dense fragment, full overlap
1: 0.000 s: - tile: row, cell: row, subarray: col
1: 0.005 s: ResultCellSlabIter: Test 2D slabs, 1 range, 1 dense fragment, full overlap
1: 0.000 s: - tile: row, cell: col, subarray: col
1: 0.004 s: ResultCellSlabIter: Test 2D slabs, 1 range, 1 dense fragment, full overlap
1: 0.000 s: - tile: col, cell: row, subarray: col
1: 0.005 s: ResultCellSlabIter: Test 2D slabs, 1 range, 1 dense fragment, full overlap
1: 0.000 s: - tile: col, cell: col, subarray: col
1: 0.005 s: ResultCellSlabIter: Test 2D slabs, 1 range, 1 dense fragment, full overlap
1: 0.000 s: - tile: row, cell: row, subarray: row
1: 0.006 s: ResultCellSlabIter: Test 2D slabs, 1 range, 1 dense fragment, no overlap
1: 0.000 s: - tile: row, cell: col, subarray: row
1: 0.005 s: ResultCellSlabIter: Test 2D slabs, 1 range, 1 dense fragment, no overlap
1: 0.000 s: - tile: col, cell: row, subarray: row
1: 0.004 s: ResultCellSlabIter: Test 2D slabs, 1 range, 1 dense fragment, no overlap
1: 0.000 s: - tile: col, cell: col, subarray: row
1: 0.004 s: ResultCellSlabIter: Test 2D slabs, 1 range, 1 dense fragment, no overlap
1: 0.000 s: - tile: row, cell: row, subarray: col
1: 0.004 s: ResultCellSlabIter: Test 2D slabs, 1 range, 1 dense fragment, no overlap
1: 0.000 s: - tile: row, cell: col, subarray: col
1: 0.004 s: ResultCellSlabIter: Test 2D slabs, 1 range, 1 dense fragment, no overlap
1: 0.000 s: - tile: col, cell: row, subarray: col
1: 0.005 s: ResultCellSlabIter: Test 2D slabs, 1 range, 1 dense fragment, no overlap
1: 0.000 s: - tile: col, cell: col, subarray: col
1: 0.004 s: ResultCellSlabIter: Test 2D slabs, 1 range, 1 dense fragment, no overlap
1: 0.000 s: - tile: row, cell: row, subarray: row
1: 0.004 s: ResultCellSlabIter: Test 2D slabs, 1 range, 1 dense fragment, partial overlap
1: 0.000 s: - tile: row, cell: col, subarray: row
1: 0.004 s: ResultCellSlabIter: Test 2D slabs, 1 range, 1 dense fragment, partial overlap
1: 0.000 s: - tile: col, cell: row, subarray: row
1: 0.005 s: ResultCellSlabIter: Test 2D slabs, 1 range, 1 dense fragment, partial overlap
1: 0.000 s: - tile: col, cell: col, subarray: row
1: 0.004 s: ResultCellSlabIter: Test 2D slabs, 1 range, 1 dense fragment, partial overlap
1: 0.000 s: - tile: row, cell: row, subarray: col
1: 0.005 s: ResultCellSlabIter: Test 2D slabs, 1 range, 1 dense fragment, partial overlap
1: 0.000 s: - tile: row, cell: col, subarray: col
1: 0.004 s: ResultCellSlabIter: Test 2D slabs, 1 range, 1 dense fragment, partial overlap
1: 0.000 s: - tile: col, cell: row, subarray: col
1: 0.004 s: ResultCellSlabIter: Test 2D slabs, 1 range, 1 dense fragment, partial overlap
1: 0.000 s: - tile: col, cell: col, subarray: col
1: 0.005 s: ResultCellSlabIter: Test 2D slabs, 1 range, 1 dense fragment, partial overlap
1: 0.000 s: - tile: row, cell: row, subarray: row
1: 0.004 s: ResultCellSlabIter: Test 2D slabs, multiple ranges, 2 denses fragments, 1 sparse overlap
1: 0.000 s: - tile: row, cell: col, subarray: row
1: 0.004 s: ResultCellSlabIter: Test 2D slabs, multiple ranges, 2 denses fragments, 1 sparse overlap
1: 0.000 s: - tile: col, cell: row, subarray: row
1: 0.004 s: ResultCellSlabIter: Test 2D slabs, multiple ranges, 2 denses fragments, 1 sparse overlap
1: 0.000 s: - tile: col, cell: col, subarray: row
1: 0.004 s: ResultCellSlabIter: Test 2D slabs, multiple ranges, 2 denses fragments, 1 sparse overlap
1: 0.000 s: - tile: row, cell: row, subarray: col
1: 0.004 s: ResultCellSlabIter: Test 2D slabs, multiple ranges, 2 denses fragments, 1 sparse overlap
1: 0.000 s: - tile: row, cell: col, subarray: col
1: 0.004 s: ResultCellSlabIter: Test 2D slabs, multiple ranges, 2 denses fragments, 1 sparse overlap
1: 0.000 s: - tile: col, cell: row, subarray: col
1: 0.004 s: ResultCellSlabIter: Test 2D slabs, multiple ranges, 2 denses fragments, 1 sparse overlap
1: 0.000 s: - tile: col, cell: col, subarray: col
1: 0.005 s: ResultCellSlabIter: Test 2D slabs, multiple ranges, 2 denses fragments, 1 sparse overlap
1: 0.000 s: RTree: Test R-Tree, basic functions
1: 0.000 s: RTree: Test 1D R-tree, height 2
1: 0.000 s: RTree: Test 1D R-tree, height 3
1: 0.000 s: RTree: Test 2D R-tree, height 2
1: 0.000 s: RTree: Test 2D R-tree, height 3
1: 0.000 s: Status: Test ok
1: 0.000 s: Status: Test code and message
1: 0.000 s: Status: Test to_string
1: 0.000 s: Status: Test code_to_string
1: 0.000 s: Status: Test posix_code
1: 0.000 s: Consolidator: Remove consolidate fragment URIs, remove none
1: 0.000 s: Consolidator: Remove consolidate fragment URIs, remove one level at start
1: 0.000 s: Consolidator: Remove consolidate fragment URIs, remove one level at middle
1: 0.000 s: Consolidator: Remove consolidate fragment URIs, remove two levels
1: 0.004 s: Subarray: Test tile coords, 1D
1: 0.000 s: tile: row
1: 0.005 s: Subarray: Test tile coords, 2D
1: 0.000 s: tile: col
1: 0.004 s: Subarray: Test tile coords, 2D
1: 0.004 s: Subarray: Test crop to tile, 2D
1: 0.004 s: SubarrayPartitioner (Dense): 1D, single-range, empty array
1: 0.011 s: SubarrayPartitioner (Dense): 1D, single-range, whole subarray fits
1: 0.012 s: SubarrayPartitioner (Dense): 1D, single-range, split once
1: 0.011 s: SubarrayPartitioner (Dense): 1D, single-range, unsplittable at once
1: 0.012 s: SubarrayPartitioner (Dense): 1D, single-range, split multiple
1: 0.012 s: SubarrayPartitioner (Dense): 1D, single-range, unsplittable after multiple
1: 0.011 s: SubarrayPartitioner (Dense): 1D, single-range, unsplittable but ok after budget reset
1: 0.012 s: SubarrayPartitioner (Dense): 1D, multi-range, whole subarray fits
1: 0.011 s: SubarrayPartitioner (Dense): 1D, multi-range, split once
1: 0.014 s: SubarrayPartitioner (Dense): 1D, multi-range, split multiple
1: 0.011 s: SubarrayPartitioner (Dense): 1D, multi-range, split multiple finer
1: 0.012 s: SubarrayPartitioner (Dense): 1D, multi-range, unsplittable
1: 0.012 s: SubarrayPartitioner (Dense): 1D, single-range, memory budget
1: 0.009 s: # tile: row, cell: row
1: 0.012 s: SubarrayPartitioner (Dense): 2D, single-range, whole subarray fits
1: 0.009 s: # tile: row, cell: col
1: 0.011 s: SubarrayPartitioner (Dense): 2D, single-range, whole subarray fits
1: 0.009 s: # tile: col, cell: row
1: 0.012 s: SubarrayPartitioner (Dense): 2D, single-range, whole subarray fits
1: 0.009 s: # tile: col, cell: col
1: 0.012 s: SubarrayPartitioner (Dense): 2D, single-range, whole subarray fits
1: 0.010 s: # tile: row, cell: row
1: 0.012 s: SubarrayPartitioner (Dense): 2D, single-range, unsplittable
1: 0.009 s: # tile: row, cell: col
1: 0.012 s: SubarrayPartitioner (Dense): 2D, single-range, unsplittable
1: 0.009 s: # tile: col, cell: row
1: 0.012 s: SubarrayPartitioner (Dense): 2D, single-range, unsplittable
1: 0.010 s: # tile: col, cell: col
1: 0.012 s: SubarrayPartitioner (Dense): 2D, single-range, unsplittable
1: 0.013 s: # tile: row, cell: row
1: 0.015 s: SubarrayPartitioner (Dense): 2D, single-range, split multiple
1: 0.009 s: # tile: row, cell: col
1: 0.012 s: SubarrayPartitioner (Dense): 2D, single-range, split multiple
1: 0.010 s: # tile: col, cell: row
1: 0.012 s: SubarrayPartitioner (Dense): 2D, single-range, split multiple
1: 0.009 s: # tile: col, cell: col
1: 0.012 s: SubarrayPartitioner (Dense): 2D, single-range, split multiple
1: 0.009 s: # tile: row, cell: row
1: 0.011 s: SubarrayPartitioner (Dense): 2D, multi-range, whole_subarray_fits
1: 0.009 s: # tile: row, cell: col
1: 0.012 s: SubarrayPartitioner (Dense): 2D, multi-range, whole_subarray_fits
1: 0.009 s: # tile: col, cell: row
1: 0.011 s: SubarrayPartitioner (Dense): 2D, multi-range, whole_subarray_fits
1: 0.011 s: # tile: col, cell: col
1: 0.013 s: SubarrayPartitioner (Dense): 2D, multi-range, whole_subarray_fits
1: 0.009 s: # tile: row, cell: row
1: 0.012 s: SubarrayPartitioner (Dense): 2D, multi-range, split once
1: 0.009 s: # tile: row, cell: col
1: 0.012 s: SubarrayPartitioner (Dense): 2D, multi-range, split once
1: 0.009 s: # tile: col, cell: row
1: 0.012 s: SubarrayPartitioner (Dense): 2D, multi-range, split once
1: 0.009 s: # tile: col, cell: col
1: 0.012 s: SubarrayPartitioner (Dense): 2D, multi-range, split once
1: 0.010 s: # tile: row, cell: row
1: 0.013 s: SubarrayPartitioner (Dense): 2D, multi-range, calibrate
1: 0.010 s: # tile: row, cell: col
1: 0.012 s: SubarrayPartitioner (Dense): 2D, multi-range, calibrate
1: 0.010 s: # tile: col, cell: row
1: 0.012 s: SubarrayPartitioner (Dense): 2D, multi-range, calibrate
1: 0.010 s: # tile: col, cell: col
1: 0.012 s: SubarrayPartitioner (Dense): 2D, multi-range, calibrate
1: 0.010 s: # tile: row, cell: row
1: 0.012 s: SubarrayPartitioner (Dense): 2D, multi-range, split multiple finer
1: 0.010 s: # tile: row, cell: col
1: 0.012 s: SubarrayPartitioner (Dense): 2D, multi-range, split multiple finer
1: 0.010 s: # tile: col, cell: row
1: 0.013 s: SubarrayPartitioner (Dense): 2D, multi-range, split multiple finer
1: 0.010 s: # tile: col, cell: col
1: 0.012 s: SubarrayPartitioner (Dense): 2D, multi-range, split multiple finer
1: 0.009 s: # tile: row, cell: row
1: 0.011 s: SubarrayPartitioner (Dense): 2D, multi-range, unsplittable
1: 0.009 s: # tile: row, cell: col
1: 0.012 s: SubarrayPartitioner (Dense): 2D, multi-range, unsplittable
1: 0.009 s: # tile: col, cell: row
1: 0.012 s: SubarrayPartitioner (Dense): 2D, multi-range, unsplittable
1: 0.010 s: # tile: col, cell: col
1: 0.012 s: SubarrayPartitioner (Dense): 2D, multi-range, unsplittable
1: 0.004 s: SubarrayPartitioner (Error): 1D, result and memory budget, setters/getters
1: 0.004 s: SubarrayPartitioner (Sparse): 1D, single-range, empty array
1: 0.013 s: SubarrayPartitioner (Sparse): 1D, single-range, whole subarray fits
1: 0.013 s: SubarrayPartitioner (Sparse): 1D, single-range, split once
1: 0.013 s: SubarrayPartitioner (Sparse): 1D, single-range, unsplittable at once
1: 0.013 s: SubarrayPartitioner (Sparse): 1D, single-range, split multiple
1: 0.013 s: SubarrayPartitioner (Sparse): 1D, single-range, unsplittable after multiple
1: 0.013 s: SubarrayPartitioner (Sparse): 1D, single-range, unsplittable but ok after budget reset
1: 0.014 s: SubarrayPartitioner (Sparse): 1D, single-range, float, split multiple
1: 0.014 s: SubarrayPartitioner (Sparse): 1D, single-range, float, unsplittable after multiple
1: 0.013 s: SubarrayPartitioner (Sparse): 1D, single-range, float, whole subarray fits
1: 0.014 s: SubarrayPartitioner (Sparse): 1D, single-range, memory budget
1: 0.013 s: SubarrayPartitioner (Sparse): 1D, multi-range, whole subarray fits
1: 0.013 s: SubarrayPartitioner (Sparse): 1D, multi-range, split once
1: 0.014 s: SubarrayPartitioner (Sparse): 1D, multi-range, split multiple
1: 0.013 s: SubarrayPartitioner (Sparse): 1D, multi-range, split multiple finer
1: 0.013 s: SubarrayPartitioner (Sparse): 1D, multi-range, unsplittable
1: 0.011 s: # tile: row, cell: row
1: 0.014 s: SubarrayPartitioner (Sparse): 2D, single-range, whole subarray fits
1: 0.011 s: # tile: row, cell: col
1: 0.013 s: SubarrayPartitioner (Sparse): 2D, single-range, whole subarray fits
1: 0.012 s: # tile: col, cell: row
1: 0.015 s: SubarrayPartitioner (Sparse): 2D, single-range, whole subarray fits
1: 0.011 s: # tile: col, cell: col
1: 0.014 s: SubarrayPartitioner (Sparse): 2D, single-range, whole subarray fits
1: 0.012 s: # tile: row, cell: row
1: 0.014 s: SubarrayPartitioner (Sparse): 2D, single-range, split multiple
1: 0.012 s: # tile: row, cell: col
1: 0.016 s: SubarrayPartitioner (Sparse): 2D, single-range, split multiple
1: 0.011 s: # tile: col, cell: row
1: 0.014 s: SubarrayPartitioner (Sparse): 2D, single-range, split multiple
1: 0.011 s: # tile: col, cell: col
1: 0.013 s: SubarrayPartitioner (Sparse): 2D, single-range, split multiple
1: 0.011 s: # tile: row, cell: row
1: 0.013 s: SubarrayPartitioner (Sparse): 2D, single-range, unsplittable
1: 0.011 s: # tile: row, cell: col
1: 0.014 s: SubarrayPartitioner (Sparse): 2D, single-range, unsplittable
1: 0.011 s: # tile: col, cell: row
1: 0.014 s: SubarrayPartitioner (Sparse): 2D, single-range, unsplittable
1: 0.011 s: # tile: col, cell: col
1: 0.013 s: SubarrayPartitioner (Sparse): 2D, single-range, unsplittable
1: 0.011 s: # tile: row, cell: row
1: 0.014 s: SubarrayPartitioner (Sparse): 2D, multi-range, whole subarray fits
1: 0.011 s: # tile: row, cell: col
1: 0.013 s: SubarrayPartitioner (Sparse): 2D, multi-range, whole subarray fits
1: 0.011 s: # tile: col, cell: row
1: 0.014 s: SubarrayPartitioner (Sparse): 2D, multi-range, whole subarray fits
1: 0.011 s: # tile: col, cell: col
1: 0.013 s: SubarrayPartitioner (Sparse): 2D, multi-range, whole subarray fits
1: 0.011 s: # tile: row, cell: row
1: 0.013 s: SubarrayPartitioner (Sparse): 2D, multi-range, split once
1: 0.011 s: # tile: row, cell: col
1: 0.014 s: SubarrayPartitioner (Sparse): 2D, multi-range, split once
1: 0.011 s: # tile: col, cell: row
1: 0.013 s: SubarrayPartitioner (Sparse): 2D, multi-range, split once
1: 0.011 s: # tile: col, cell: col
1: 0.013 s: SubarrayPartitioner (Sparse): 2D, multi-range, split once
1: 0.011 s: # tile: row, cell: row
1: 0.013 s: SubarrayPartitioner (Sparse): 2D, multi-range, calibrate
1: 0.011 s: # tile: row, cell: col
1: 0.013 s: SubarrayPartitioner (Sparse): 2D, multi-range, calibrate
1: 0.011 s: # tile: col, cell: row
1: 0.013 s: SubarrayPartitioner (Sparse): 2D, multi-range, calibrate
1: 0.010 s: # tile: col, cell: col
1: 0.013 s: SubarrayPartitioner (Sparse): 2D, multi-range, calibrate
1: 0.011 s: # tile: row, cell: row
1: 0.014 s: SubarrayPartitioner (Sparse): 2D, multi-range, unsplittable
1: 0.039 s: # tile: row, cell: col
1: 0.041 s: SubarrayPartitioner (Sparse): 2D, multi-range, unsplittable
1: 0.011 s: # tile: col, cell: row
1: 0.014 s: SubarrayPartitioner (Sparse): 2D, multi-range, unsplittable
1: 0.011 s: # tile: col, cell: col
1: 0.014 s: SubarrayPartitioner (Sparse): 2D, multi-range, unsplittable
1: 0.012 s: # tile: row, cell: row
1: 0.014 s: SubarrayPartitioner (Sparse): 2D, multi-range, split multiple finer
1: 0.012 s: # tile: row, cell: col
1: 0.014 s: SubarrayPartitioner (Sparse): 2D, multi-range, split multiple finer
1: 0.012 s: # tile: col, cell: row
1: 0.014 s: SubarrayPartitioner (Sparse): 2D, multi-range, split multiple finer
1: 0.012 s: # tile: col, cell: col
1: 0.014 s: SubarrayPartitioner (Sparse): 2D, multi-range, split multiple finer
1: 0.001 s: TileDB TBB negative number of set threads
1: 0.002 s: TileDB TBB different number of set threads per process
1: 0.002 s: ThreadPool: Test empty
1: 0.000 s: ThreadPool: Test single thread
1: 0.001 s: ThreadPool: Test multiple threads
1: 0.002 s: ThreadPool: Test wait status
1: 1.000 s: ThreadPool: Test no wait
1: 0.000 s: - No cancellation callback
1: 0.000 s: ThreadPool: Test pending task cancellation
1: 0.000 s: - With cancellation callback
1: 0.000 s: ThreadPool: Test pending task cancellation
1: 0.000 s: ThreadPool: Test enqueue with empty pool
1: 0.000 s: TileDomain: Test 1D
1: 0.000 s: TileDomain: Test 2D, row-major, complete
1: 0.000 s: TileDomain: Test 2D, row-major, partial
1: 0.000 s: TileDomain: Test 2D, col-major, complete
1: 0.000 s: TileDomain: Test 2D, col-major, partial
1: 0.000 s: TileDomain: Test 2D, tile subarray
1: 0.000 s: TileDomain: Test 2D, tile overlap
1: 0.000 s: TileDomain: Test 2D, in tile domain
1: 0.000 s: TileDomain: Test 2D, covers
1: 0.000 s: URI: Test join
1: 0.000 s: URI: Test file URIs
1: 0.000 s: URI: Test relative paths
1: 0.000 s: URI: Test URI to path
1: 0.000 s: URI: Test schemes
1: 0.000 s: URI: Test REST components
1: 0.000 s: - Serial
1: 0.000 s: UUID: Test generate
1: 0.002 s: - Threaded
1: 0.002 s: UUID: Test generate
1: 0.000 s: - Default config
1: 0.001 s: VFS: Test read batching
1: 0.001 s: - Reduce min batch size and min batch gap
1: 0.001 s: VFS: Test read batching
1: 0.000 s: - Reduce min batch size but not min batch gap
1: 0.001 s: VFS: Test read batching
1: 0.000 s: - Reduce min batch gap but not min batch size
1: 0.001 s: VFS: Test read batching
1: 0.003 s: - Deep hierarchy
1: 0.024 s: VFS: Test long posix paths
1: 0.000 s: - Too long name
1: 0.000 s: VFS: Test long posix paths
1: 0.000 s: Config
1: 0.000 s: Dimensions
1: 0.004 s: C++ API: Arrays
1: 0.000 s: Make Buffer
1: 0.003 s: C++ API: Arrays
1: 0.015 s: Read/Write
1: 0.019 s: C++ API: Arrays
1: 0.014 s: Global order write
1: 0.018 s: C++ API: Arrays
1: 0.000 s: Global order write - no dummy values
1: 0.003 s: C++ API: Arrays
1: 0.003 s: C++ API: Incorrect buffer size and offsets
1: 0.120 s: C++ API: Read subarray with expanded domain
1: 0.004 s: C++ API: Consolidation of empty arrays
1: 0.020 s: C++ API: Consolidation of sequential fragment writes
1: 0.013 s: C++ API: Encrypted array
1: 0.012 s: C++ API: Encrypted array, std::string key
1: 0.003 s: C++ API: Open array with anonymous attribute
1: 0.000 s: Testing Array::Array
1: 0.008 s: C++ API: Open array at
1: 0.000 s: Testing Array::open
1: 0.008 s: C++ API: Open array at
1: 0.000 s: Testing Array::Array
1: 0.008 s: C++ API: Open array at
1: 0.000 s: Testing Array::open
1: 0.008 s: C++ API: Open array at
1: 0.000 s: Testing Array::Array
1: 0.008 s: C++ API: Open encrypted array at
1: 0.000 s: Testing Array::open
1: 0.008 s: C++ API: Open encrypted array at
1: 0.000 s: Testing Array::Array
1: 0.008 s: C++ API: Open encrypted array at
1: 0.000 s: Testing Array::open
1: 0.008 s: C++ API: Open encrypted array at
1: 0.009 s: C++ API: Writing single cell with global order
1: 0.057 s: C++ API: Write cell with large cell val num
1: 0.000 s: C++ API: Config
1: 0.000 s: C++ API: Config iterator
1: 0.010 s: C++ API: Datetime attribute
1: 0.010 s: C++ API: Datetime dimension
1: 0.001 s: C++ API: Filter options
1: 0.001 s: C++ API: Filter lists
1: 0.014 s: C++ API: Filter lists on array
1: 0.035 s: C++ API: Map
1: 0.018 s: C++ API: Map Issue 606 segault in Reader::zero_out_buffer_sizes()
1: 0.012 s: C++ API: Map, implicit attribute
1: 0.015 s: C++ API: Map from std::map
1: 0.016 s: C++ API: Map iter
1: 0.035 s: C++ API: Encrypted map
1: 0.000 s: Testing Map::Map
1: 0.014 s: C++ API: Open map at
1: 0.000 s: Testing Map::open
1: 0.014 s: C++ API: Open map at
1: 0.000 s: Testing Map::Map
1: 0.014 s: C++ API: Open map at
1: 0.000 s: Testing Map::open
1: 0.014 s: C++ API: Open map at
1: 0.000 s: Testing Map::Map
1: 0.014 s: C++ API: Open encrypted map at
1: 0.000 s: Testing Map::open
1: 0.014 s: C++ API: Open encrypted map at
1: 0.000 s: Testing Map::Map
1: 0.014 s: C++ API: Open encrypted map at
1: 0.000 s: Testing Map::open
1: 0.014 s: C++ API: Open encrypted map at
1: 0.004 s: C++ API: Test get query layout
1: 0.000 s: Dense Array Schema
1: 0.001 s: C++ API: Schema
1: 0.000 s: Sparse Array Schema
1: 0.001 s: C++ API: Schema
1: 0.000 s: Map Schema
1: 0.001 s: C++ API: Schema
1: 0.000 s: Invalid dimension types
1: 0.001 s: C++ API: Schema
1: 0.002 s: C++ API: Test schema virtual destructors
1: 0.001 s: - Read single cell
1: 0.010 s: C++ API: Test subarray
1: 0.001 s: - Read single range
1: 0.010 s: C++ API: Test subarray
1: 0.001 s: - Read two cells
1: 0.010 s: C++ API: Test subarray
1: 0.001 s: - Read two regions
1: 0.010 s: C++ API: Test subarray
1: 0.010 s: C++ API: Test subarray (incomplete)
1: 0.009 s: C++ API: Test subarray (incomplete overlapping)
1: 0.001 s: C++ API: Types
1: 0.015 s: C++ API updates: test writing two identical fragments
1: 0.000 s: Group by cell, offset
1: 0.000 s: C++ API: Utils
1: 0.000 s: Group by cell, fixed
1: 0.000 s: C++ API: Utils
1: 0.000 s: Group by cell, dynamic
1: 0.000 s: C++ API: Utils
1: 0.000 s: Group by cell, int values
1: 0.000 s: C++ API: Utils
1: 0.000 s: Unpack var buffer
1: 0.000 s: C++ API: Utils
1: 0.000 s: Ungroup-group is idempotent
1: 0.000 s: C++ API: Utils
1: 0.000 s: Flatten
1: 0.000 s: C++ API: Utils
1: 0.002 s: C++ API: Test VFS ls
1: 0.008 s: C++ API: Test VFS dir size
1: ===============================================================================
1: All tests passed (2636783 assertions in 371 test cases)
1:
1/1 Test #1: tiledb_unit ......................   Passed   33.68 sec

100% tests passed, 0 tests failed out of 1

Total Test time (real) =  33.69 sec
[100%] Built target chec
@Rakesh4G

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commented Sep 4, 2019

log below

Hi @ihnorton , I have compared logs in #67187 (comment) with my logs. There are no visible differences. Thanks.

@ihnorton

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commented Sep 4, 2019

The general differences I can see are:

  • CPU: however, if I understand correctly, they are both Ryzen generation
  • you are using ZFS. It's hard to imagine this could be the problem without much larger problems manifesting elsewhere (TileDB is using POSIX file operations)
  • NixOS unstable version -- just tested in nixos-19.09pre191505.7d5375ebf4c-x86_64-linux.ova in a local VM: still works fine.

It's clear something strange is happening, we're just not sure how else to debug it at this point.

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commented Sep 4, 2019

Also, just to note, the following patch allows the package build to complete successfully for me:

diff --git a/pkgs/development/libraries/tiledb/default.nix b/pkgs/development/libraries/tiledb/default.nix
index 3c0a4d02c9e..0cb4108486e 100644
--- a/pkgs/development/libraries/tiledb/default.nix
+++ b/pkgs/development/libraries/tiledb/default.nix
@@ -36,6 +36,8 @@ stdenv.mkDerivation {
 
   makeTarget = "tiledb";
 
+  installTargets = "install-tiledb";
+
   nativeBuildInputs = [clang-tools cmake doxygen  gtest];
 
   buildInputs = [ catch2 zlib lz4 bzip2 zstd spdlog_0 tbb openssl boost libpqxx python ];
@Rakesh4G

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commented Sep 5, 2019

Also, just to note, the following patch allows the package build to complete successfully for me:

diff --git a/pkgs/development/libraries/tiledb/default.nix b/pkgs/development/libraries/tiledb/default.nix
index 3c0a4d02c9e..0cb4108486e 100644
--- a/pkgs/development/libraries/tiledb/default.nix
+++ b/pkgs/development/libraries/tiledb/default.nix
@@ -36,6 +36,8 @@ stdenv.mkDerivation {
 
   makeTarget = "tiledb";
 
+  installTargets = "install-tiledb";
+
   nativeBuildInputs = [clang-tools cmake doxygen  gtest];
 
   buildInputs = [ catch2 zlib lz4 bzip2 zstd spdlog_0 tbb openssl boost libpqxx python ];

Thanks @ihnorton . I will update this change.

Rakesh4G added 3 commits Sep 5, 2019
@lheckemann lheckemann added this to the 20.03 milestone Sep 12, 2019
@CMCDragonkai

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commented Sep 23, 2019

I'm testing the build of this as well, and I noticed when enabling make check, it doesn't use all the cores. Now I see that in this documentation https://github.com/Intel-HLS/TileDB/wiki/Building-TileDB we can use -j to set the number of parallel cores. Is there a corresponding setting here for Nix builds when using make check? Because all my other builds use all cores when monitoring htop.

Also I can corroborate and reproduce the errors experienced by @Rakesh4G.

The final output after enabling make check is this section:

===============================================================================
test cases:     371 |     365 passed |   6 failed
assertions: 1562231 | 1562125 passed | 106 failed



0% tests passed, 1 tests failed out of 1

Total Test time (real) =  19.37 sec

The following tests FAILED:
          1 - tiledb_unit (Failed)
Errors while running CTest
make[7]: *** [test/CMakeFiles/check.dir/build.make:57: test/CMakeFiles/check] Error 8
make[6]: *** [CMakeFiles/Makefile2:1880: test/CMakeFiles/check.dir/all] Error 2
make[5]: *** [CMakeFiles/Makefile2:1887: test/CMakeFiles/check.dir/rule] Error 2
make[4]: *** [Makefile:942: check] Error 2
make[3]: *** [CMakeFiles/check.dir/build.make:57: CMakeFiles/check] Error 2
make[2]: *** [CMakeFiles/Makefile2:161: CMakeFiles/check.dir/all] Error 2
make[1]: *** [CMakeFiles/Makefile2:168: CMakeFiles/check.dir/rule] Error 2
make: *** [Makefile:157: check] Error 2
builder for '/nix/store/1lrag40zjjygjhd505rs8vxkr5ifafxx-tiledb.drv' failed with exit code 2
error: build of '/nix/store/1lrag40zjjygjhd505rs8vxkr5ifafxx-tiledb.drv' failed
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commented Sep 23, 2019

I also get non-deterministic errors. Second time running:

===============================================================================
test cases:     371 |     366 passed |  5 failed
assertions: 1545280 | 1545213 passed | 67 failed



0% tests passed, 1 tests failed out of 1

Total Test time (real) =  19.77 sec

The following tests FAILED:
          1 - tiledb_unit (Failed)
Errors while running CTest
make[7]: *** [test/CMakeFiles/check.dir/build.make:57: test/CMakeFiles/check] Error 8
make[6]: *** [CMakeFiles/Makefile2:1880: test/CMakeFiles/check.dir/all] Error 2
make[5]: *** [CMakeFiles/Makefile2:1887: test/CMakeFiles/check.dir/rule] Error 2
make[4]: *** [Makefile:942: check] Error 2
make[3]: *** [CMakeFiles/check.dir/build.make:57: CMakeFiles/check] Error 2
make[2]: *** [CMakeFiles/Makefile2:161: CMakeFiles/check.dir/all] Error 2
make[1]: *** [CMakeFiles/Makefile2:168: CMakeFiles/check.dir/rule] Error 2
make: *** [Makefile:157: check] Error 2
builder for '/nix/store/1lrag40zjjygjhd505rs8vxkr5ifafxx-tiledb.drv' failed with exit code 2
error: build of '/nix/store/1lrag40zjjygjhd505rs8vxkr5ifafxx-tiledb.drv' failed

Could there be something random that needs to be set statically during the build/check phase?

Some snippets of where the errors are:

-------------------------------------------------------------------------------
C API: Test 1d dense vector
-------------------------------------------------------------------------------
/build/TileDB-0eb1eba/test/src/unit-capi-dense_vector.cc:475
...............................................................................

/build/TileDB-0eb1eba/test/src/unit-capi-dense_vector.cc:471: FAILED:
  CHECK( (buffer[0] == num_writes - 1 && buffer[1] == num_writes - 1 && buffer[2] == num_writes - 1) )
with expansion:
  false
-------------------------------------------------------------------------------
C API: Test dense array, multi-fragment reads
-------------------------------------------------------------------------------
/build/TileDB-0eb1eba/test/src/unit-capi-dense_array.cc:3912
...............................................................................

/build/TileDB-0eb1eba/test/src/unit-capi-dense_array.cc:4013: FAILED:
  CHECK( !memcmp(c_a, read_a, sizeof(c_a)) )
with expansion:
  false
-------------------------------------------------------------------------------
C API: Test advanced consolidation, overwritten fragments, deletion #1
-------------------------------------------------------------------------------
/build/TileDB-0eb1eba/test/src/unit-capi-consolidation.cc:4035
...............................................................................

/build/TileDB-0eb1eba/test/src/unit-capi-consolidation.cc:2193: FAILED:
  CHECK( a[i] == c_a[i] )
with expansion:
  1251 (0x4e3) == 250

/build/TileDB-0eb1eba/test/src/unit-capi-consolidation.cc:2193: FAILED:
  CHECK( a[i] == c_a[i] )
with expansion:
  1276 (0x4fc) == 275 (0x113)

/build/TileDB-0eb1eba/test/src/unit-capi-consolidation.cc:2193: FAILED:
  CHECK( a[i] == c_a[i] )
with expansion:
  1301 (0x515) == 300 (0x12c)

/build/TileDB-0eb1eba/test/src/unit-capi-consolidation.cc:4074: FAILED:
  CHECK( data.dir_num == 1 )
with expansion:
  2 == 1
-------------------------------------------------------------------------------
C API: Test consolidation, fragments that don't coincide with space tiles #1
-------------------------------------------------------------------------------
/build/TileDB-0eb1eba/test/src/unit-capi-consolidation.cc:3722
...............................................................................

/build/TileDB-0eb1eba/test/src/unit-capi-consolidation.cc:1883: FAILED:
  CHECK( a[i] == c_a[i] )
with expansion:
  -2147483648 == 248

/build/TileDB-0eb1eba/test/src/unit-capi-consolidation.cc:1883: FAILED:
  CHECK( a[i] == c_a[i] )
with expansion:
  -2147483648 == 249

/build/TileDB-0eb1eba/test/src/unit-capi-consolidation.cc:1883: FAILED:
  CHECK( a[i] == c_a[i] )
with expansion:
  -2147483648 == 250

/build/TileDB-0eb1eba/test/src/unit-capi-consolidation.cc:1883: FAILED:
  CHECK( a[i] == c_a[i] )
with expansion:
  -2147483648 == 251

/build/TileDB-0eb1eba/test/src/unit-capi-consolidation.cc:1883: FAILED:
  CHECK( a[i] == c_a[i] )
with expansion:
  -2147483648 == 252

/build/TileDB-0eb1eba/test/src/unit-capi-consolidation.cc:1883: FAILED:
  CHECK( a[i] == c_a[i] )
with expansion:
  -2147483648 == 253

/build/TileDB-0eb1eba/test/src/unit-capi-consolidation.cc:1883: FAILED:
  CHECK( a[i] == c_a[i] )
with expansion:
  -2147483648 == 254

/build/TileDB-0eb1eba/test/src/unit-capi-consolidation.cc:1883: FAILED:
  CHECK( a[i] == c_a[i] )
with expansion:
  -2147483648 == 255

/build/TileDB-0eb1eba/test/src/unit-capi-consolidation.cc:1883: FAILED:
  CHECK( a[i] == c_a[i] )
with expansion:
  -2147483648 == 256 (0x100)

/build/TileDB-0eb1eba/test/src/unit-capi-consolidation.cc:1883: FAILED:
  CHECK( a[i] == c_a[i] )
with expansion:
  -2147483648 == 257 (0x101)

/build/TileDB-0eb1eba/test/src/unit-capi-consolidation.cc:1883: FAILED:
  CHECK( a[i] == c_a[i] )
with expansion:
  -2147483648 == 258 (0x102)

/build/TileDB-0eb1eba/test/src/unit-capi-consolidation.cc:1883: FAILED:
  CHECK( a[i] == c_a[i] )
with expansion:
  -2147483648 == 259 (0x103)

/build/TileDB-0eb1eba/test/src/unit-capi-consolidation.cc:1883: FAILED:
  CHECK( a[i] == c_a[i] )
with expansion:
  -2147483648 == 260 (0x104)

/build/TileDB-0eb1eba/test/src/unit-capi-consolidation.cc:1883: FAILED:
  CHECK( a[i] == c_a[i] )
with expansion:
  -2147483648 == 261 (0x105)

/build/TileDB-0eb1eba/test/src/unit-capi-consolidation.cc:1883: FAILED:
  CHECK( a[i] == c_a[i] )
with expansion:
  -2147483648 == 262 (0x106)

/build/TileDB-0eb1eba/test/src/unit-capi-consolidation.cc:1883: FAILED:
  CHECK( a[i] == c_a[i] )
with expansion:
  -2147483648 == 263 (0x107)

/build/TileDB-0eb1eba/test/src/unit-capi-consolidation.cc:1883: FAILED:
  CHECK( a[i] == c_a[i] )
with expansion:
  -2147483648 == 264 (0x108)

/build/TileDB-0eb1eba/test/src/unit-capi-consolidation.cc:1883: FAILED:
  CHECK( a[i] == c_a[i] )
with expansion:
  -2147483648 == 265 (0x109)

/build/TileDB-0eb1eba/test/src/unit-capi-consolidation.cc:1883: FAILED:
  CHECK( a[i] == c_a[i] )
with expansion:
  -2147483648 == 266 (0x10a)

/build/TileDB-0eb1eba/test/src/unit-capi-consolidation.cc:1883: FAILED:
  CHECK( a[i] == c_a[i] )
with expansion:
  -2147483648 == 267 (0x10b)

/build/TileDB-0eb1eba/test/src/unit-capi-consolidation.cc:1883: FAILED:
  CHECK( a[i] == c_a[i] )
with expansion:
  -2147483648 == 268 (0x10c)

/build/TileDB-0eb1eba/test/src/unit-capi-consolidation.cc:1883: FAILED:
  CHECK( a[i] == c_a[i] )
with expansion:
  -2147483648 == 269 (0x10d)

/build/TileDB-0eb1eba/test/src/unit-capi-consolidation.cc:1883: FAILED:
  CHECK( a[i] == c_a[i] )
with expansion:
  -2147483648 == 270 (0x10e)

/build/TileDB-0eb1eba/test/src/unit-capi-consolidation.cc:1883: FAILED:
  CHECK( a[i] == c_a[i] )
with expansion:
  -2147483648 == 271 (0x10f)

/build/TileDB-0eb1eba/test/src/unit-capi-consolidation.cc:1883: FAILED:
  CHECK( a[i] == c_a[i] )
with expansion:
  -2147483648 == 272 (0x110)

/build/TileDB-0eb1eba/test/src/unit-capi-consolidation.cc:1883: FAILED:
  CHECK( a[i] == c_a[i] )
with expansion:
  -2147483648 == 273 (0x111)

/build/TileDB-0eb1eba/test/src/unit-capi-consolidation.cc:1883: FAILED:
  CHECK( a[i] == c_a[i] )
with expansion:
  -2147483648 == 274 (0x112)

/build/TileDB-0eb1eba/test/src/unit-capi-consolidation.cc:1883: FAILED:
  CHECK( a[i] == c_a[i] )
with expansion:
  -2147483648 == 275 (0x113)

/build/TileDB-0eb1eba/test/src/unit-capi-consolidation.cc:1883: FAILED:
  CHECK( a[i] == c_a[i] )
with expansion:
  -2147483648 == 276 (0x114)

/build/TileDB-0eb1eba/test/src/unit-capi-consolidation.cc:1883: FAILED:
  CHECK( a[i] == c_a[i] )
with expansion:
  -2147483648 == 277 (0x115)

/build/TileDB-0eb1eba/test/src/unit-capi-consolidation.cc:1883: FAILED:
  CHECK( a[i] == c_a[i] )
with expansion:
  -2147483648 == 278 (0x116)

/build/TileDB-0eb1eba/test/src/unit-capi-consolidation.cc:1883: FAILED:
  CHECK( a[i] == c_a[i] )
with expansion:
  -2147483648 == 279 (0x117)

/build/TileDB-0eb1eba/test/src/unit-capi-consolidation.cc:1883: FAILED:
  CHECK( a[i] == c_a[i] )
with expansion:
  -2147483648 == 280 (0x118)

/build/TileDB-0eb1eba/test/src/unit-capi-consolidation.cc:1883: FAILED:
  CHECK( a[i] == c_a[i] )
with expansion:
  -2147483648 == 281 (0x119)

/build/TileDB-0eb1eba/test/src/unit-capi-consolidation.cc:1883: FAILED:
  CHECK( a[i] == c_a[i] )
with expansion:
  -2147483648 == 282 (0x11a)

/build/TileDB-0eb1eba/test/src/unit-capi-consolidation.cc:1883: FAILED:
  CHECK( a[i] == c_a[i] )
with expansion:
  -2147483648 == 283 (0x11b)

/build/TileDB-0eb1eba/test/src/unit-capi-consolidation.cc:1883: FAILED:
  CHECK( a[i] == c_a[i] )
with expansion:
  -2147483648 == 284 (0x11c)

/build/TileDB-0eb1eba/test/src/unit-capi-consolidation.cc:1883: FAILED:
  CHECK( a[i] == c_a[i] )
with expansion:
  -2147483648 == 285 (0x11d)

/build/TileDB-0eb1eba/test/src/unit-capi-consolidation.cc:1883: FAILED:
  CHECK( a[i] == c_a[i] )
with expansion:
  -2147483648 == 286 (0x11e)

/build/TileDB-0eb1eba/test/src/unit-capi-consolidation.cc:1883: FAILED:
  CHECK( a[i] == c_a[i] )
with expansion:
  -2147483648 == 287 (0x11f)

/build/TileDB-0eb1eba/test/src/unit-capi-consolidation.cc:1883: FAILED:
  CHECK( a[i] == c_a[i] )
with expansion:
  -2147483648 == 288 (0x120)

/build/TileDB-0eb1eba/test/src/unit-capi-consolidation.cc:1883: FAILED:
  CHECK( a[i] == c_a[i] )
with expansion:
  -2147483648 == 289 (0x121)

/build/TileDB-0eb1eba/test/src/unit-capi-consolidation.cc:1883: FAILED:
  CHECK( a[i] == c_a[i] )
with expansion:
  -2147483648 == 290 (0x122)

/build/TileDB-0eb1eba/test/src/unit-capi-consolidation.cc:1883: FAILED:
  CHECK( a[i] == c_a[i] )
with expansion:
  -2147483648 == 291 (0x123)

/build/TileDB-0eb1eba/test/src/unit-capi-consolidation.cc:1883: FAILED:
  CHECK( a[i] == c_a[i] )
with expansion:
  -2147483648 == 292 (0x124)

/build/TileDB-0eb1eba/test/src/unit-capi-consolidation.cc:1883: FAILED:
  CHECK( a[i] == c_a[i] )
with expansion:
  -2147483648 == 293 (0x125)

/build/TileDB-0eb1eba/test/src/unit-capi-consolidation.cc:1883: FAILED:
  CHECK( a[i] == c_a[i] )
with expansion:
  -2147483648 == 294 (0x126)

/build/TileDB-0eb1eba/test/src/unit-capi-consolidation.cc:1883: FAILED:
  CHECK( a[i] == c_a[i] )
with expansion:
  -2147483648 == 295 (0x127)

/build/TileDB-0eb1eba/test/src/unit-capi-consolidation.cc:1883: FAILED:
  CHECK( a[i] == c_a[i] )
with expansion:
  -2147483648 == 296 (0x128)

/build/TileDB-0eb1eba/test/src/unit-capi-consolidation.cc:1883: FAILED:
  CHECK( a[i] == c_a[i] )
with expansion:
  -2147483648 == 297 (0x129)

/build/TileDB-0eb1eba/test/src/unit-capi-consolidation.cc:1883: FAILED:
  CHECK( a[i] == c_a[i] )
with expansion:
  -2147483648 == 298 (0x12a)

/build/TileDB-0eb1eba/test/src/unit-capi-consolidation.cc:1883: FAILED:
  CHECK( a[i] == c_a[i] )
with expansion:
  -2147483648 == 299 (0x12b)

/build/TileDB-0eb1eba/test/src/unit-capi-consolidation.cc:1883: FAILED:
  CHECK( a[i] == c_a[i] )
with expansion:
  -2147483648 == 300 (0x12c)

/build/TileDB-0eb1eba/test/src/unit-capi-consolidation.cc:1883: FAILED:
  CHECK( a[i] == c_a[i] )
with expansion:
  -2147483648 == 301 (0x12d)

/build/TileDB-0eb1eba/test/src/unit-capi-consolidation.cc:1883: FAILED:
  CHECK( a[i] == c_a[i] )
with expansion:
  -2147483648 == 302 (0x12e)

/build/TileDB-0eb1eba/test/src/unit-capi-consolidation.cc:1883: FAILED:
  CHECK( a[i] == c_a[i] )
with expansion:
  -2147483648 == 303 (0x12f)

/build/TileDB-0eb1eba/test/src/unit-capi-consolidation.cc:1883: FAILED:
  CHECK( a[i] == c_a[i] )
with expansion:
  -2147483648 == 304 (0x130)

/build/TileDB-0eb1eba/test/src/unit-capi-consolidation.cc:1883: FAILED:
  CHECK( a[i] == c_a[i] )
with expansion:
  -2147483648 == 305 (0x131)

/build/TileDB-0eb1eba/test/src/unit-capi-consolidation.cc:1883: FAILED:
  CHECK( a[i] == c_a[i] )
with expansion:
  -2147483648 == 306 (0x132)

/build/TileDB-0eb1eba/test/src/unit-capi-consolidation.cc:1883: FAILED:
  CHECK( a[i] == c_a[i] )
with expansion:
  -2147483648 == 307 (0x133)
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commented Sep 23, 2019

Looks like the errors are coming from unit-capi-consolidation.cc and unit-capi-dense_array.cc and unit-capi-dense_vector.cc.

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commented Sep 23, 2019

If we look at just the consolidation errors. These appear to be failing because there is a check on a number. Specifically: CHECK( a[i] == c_a[i] ). Notice that they are all variations of -2147483648 == XXX. Now -2147483648 is a full 32 bit of 11111111111111111111111111111111. Maybe this some sort of bitwise or type error?

Cosmic bitflips? Unlikely. There does seem to be a pattern to these errors.

@ihnorton I also use Ryzen 7 CPUs.

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commented Sep 23, 2019

@CMCDragonkai are you also running on ZFS?

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commented Sep 23, 2019

Now I see that in this documentation https://github.com/Intel-HLS/TileDB/wiki/Building-TileDB we can use -j to set the number of parallel cores. Is there a corresponding setting here for Nix builds when using make check? Because all my other builds use all cores when monitoring htop.

Just a reminder that the correct docs can be found at: https://docs.tiledb.io/en/stable/. The official TileDB repo is https://github.com/TileDB-Inc/TileDB.

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commented Sep 23, 2019

I'm testing the build of this as well, and I noticed when enabling make check, it doesn't use all the cores. Now I see that in this documentation https://github.com/Intel-HLS/TileDB/wiki/Building-TileDB we can use -j to set the number of parallel cores. Is there a corresponding setting here for Nix builds when using make check? Because all my other builds use all cores when monitoring htop.

You want enableParallelBuilding = true; in the expression. This should pass -j $NIX_BUILD_CORES to nix-build. https://nixos.org/nix/manual/#chap-tuning-cores-and-jobs for more info

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commented Sep 24, 2019

Yes I'm also running ZFS. Do you think tiledb doesn't work on ZFS/Ryzen?

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commented Sep 27, 2019

Hi @CMCDragonkai, up until now I don't know of anyone else who has tested TileDB on ZFS. However, I just ran some tests with the build and test directories stored on a ZFS partition (attached to the same AMD EPYC / Amazon EC2 instance -- m4a.2xlarge instance type with ubuntu 18.04 host; 8 cores; 32 GB RAM). All of the tests succeeded:

  • 64 runs of the full test suite with 4 x 16 parallelism (CPUs were pegged at 100% most of the time)
  • 1000 runs of the consolidation tests only, with 8x parallelism (the consolidation tests seem to be the most problematic in the logs you and @Rakesh4G have posted)

The above was a standalone build using the default ubuntu toolchain.

I also reinstalled nix-shell with the ZFS partition as /nix, and nixpkgs under /nix/nixpkgs. Then I ran nix-env -f /nix/nixpkgs -iA tiledb (as in this comment), and all tests succeeded. I only ran this once, as I'm not sure where nix-build puts the tiledb_unit executable (perhaps it only saves the install by-products).

Given the above, it seems the remaining variables I cannot replicate are:

  • Ryzen (it is unclear to me what is the exact difference between your Ryzen model and the AMD EPYC 7571 CPU I have)
  • native NixOS plus ZFS (rather than only nix-shell)

If there is any possibility to give me remote access to such a system as you are using, I could try to debug further that way. (if that is a possibility, and you want to contact me off-github, please email isaiah {at} tiledb.io)

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commented Sep 27, 2019

Oh, one additional thought. By default, TileDB uses Intel TBB for parallelism. It may be worth testing with TBB disabled by adding cmakeFlags = [ "-DTILEDB_TBB=OFF" ]; to the build expression.

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commented Sep 30, 2019

Oh, one additional thought. By default, TileDB uses Intel TBB for parallelism. It may be worth testing with TBB disabled by adding cmakeFlags = [ "-DTILEDB_TBB=OFF" ]; to the build expression.

ok, @ihnorton , I will try this. Thanks.

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commented Sep 30, 2019

Oh, one additional thought. By default, TileDB uses Intel TBB for parallelism. It may be worth testing with TBB disabled by adding cmakeFlags = [ "-DTILEDB_TBB=OFF" ]; to the build expression.

hi @ihnorton ,

tiledb Tests are still failing even after cmakeFlags = [ "-DTILEDB_TBB=OFF" ];
Thanks.

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