Installation

[OZTaekOppa]

Hi,

I am trying to install this program on HPC (PBSpro) but not sure which part I should follow.
And, I have tried "Developing with conan" and "Pre commit".

FYI, this is what I did.

conda activate pip and cmake

git clone https://github.com/nanoporetech/pod5-file-format.git
cd pod5-file-format
git submodule update --init --recursive
mkdir build
cd build

conan install --build=missing -s build_type=Release ..
cmake -DUSE_CONAN=ON -DCMAKE_BUILD_TYPE=Release ..

Both attempts were not successful due to the cmake step.

ERROR: boost/1.78.0: Error in build() method, line 875
self.run(full_command, run_environment=True)
ConanException: Error 1 while executing b2 -q target-os=linux architecture=x86 address-model=64 binary-format=elf abi=sysv --layout=system --user-config=/home/uqhjung3/.conan/data/boost/1.78.0///source/source_subfolder/tools/build/user-config.jam -sNO_ZLIB=0 -sNO_BZIP2=0 -sNO_LZMA=1 -sNO_ZSTD=1 boost.locale.icu=off --disable-icu boost.locale.iconv=on boost.locale.iconv.lib=libc threading=multi visibility=hidden link=static variant=release --with-atomic --with-chrono --with-container --with-context --with-contract --with-coroutine --with-date_time --with-exception --with-filesystem --with-iostreams --with-locale --with-log --with-program_options --with-random --with-regex --with-serialization --with-stacktrace --with-system --with-test --with-thread --with-timer --with-type_erasure --with-wave toolset=gcc define=GLIBCXX_USE_CXX11_ABI=0 pch=on cxxflags="-fPIC -DBOOST_STACKTRACE_ADDR2LINE_LOCATION=/usr/bin/addr2line" install --prefix=/home/uqhjung3/.conan/data/boost/1.78.0///package/cf5b1011055d170fc18a05ba048979d2089d1695 -j24 --abbreviate-paths -d0 --debug-configuration --build-dir="/home/uqhjung3/.conan/data/boost/1.78.0//_/build/cf5b1011055d170fc18a05ba048979d2089d1695"

Any idea or suggestion on this matter?

Many thanks in advance!

Taek

[0x55555555]

Hi @OZTaekOppa,

Some of the error above in conan has been lost - can you try to post more of the error?

It looks like your system is failing to build boost as part of the conan install step, something inside b2...

If you can post a more complete log of the output I can try to work out whats going on for you.

Thanks,

• George

[OZTaekOppa]

Hi,

Here is the full list that I have tried.
Please see the attached file.

Pod5_Issue.txt

I have activated the pip and cmake from bioconda environment.

Cheers,

Taek

[0x55555555]

Hi @OZTaekOppa ,

The critical section of the log seems to be:

<compileflags>"-I/home/uqhjung3/.conan/data/libbacktrace/cci.20210118/_/_/package/3a5f72c8cd50641b8efa6ed13e6914c6ced2747c/include" <linkflags>"-L/home/uqhjung3/.conan/data/libbacktrace/cci.20210118/_/_/package/3a5f72c8cd50641b8efa6ed13e6914c6ced2747c/lib"  ;
boost/1.78.0: WARN: b2 -q target-os=linux architecture=x86 address-model=64 binary-format=elf abi=sysv --layout=system --user-config=/home/uqhjung3/.conan/data/boost/1.78.0/_/_/source/source_subfolder/tools/build/user-config.jam -sNO_ZLIB=0 -sNO_BZIP2=0 -sNO_LZMA=1 -sNO_ZSTD=1 boost.locale.icu=off --disable-icu boost.locale.iconv=on boost.locale.iconv.lib=libc threading=multi visibility=hidden link=static variant=release --with-atomic --with-chrono --with-container --with-context --with-contract --with-coroutine --with-date_time --with-exception --with-filesystem --with-iostreams --with-locale --with-log --with-program_options --with-random --with-regex --with-serialization --with-stacktrace --with-system --with-test --with-thread --with-timer --with-type_erasure --with-wave toolset=gcc define=_GLIBCXX_USE_CXX11_ABI=0 pch=on  cxxflags="-fPIC -DBOOST_STACKTRACE_ADDR2LINE_LOCATION=/usr/bin/addr2line" install --prefix=/home/uqhjung3/.conan/data/boost/1.78.0/_/_/package/cf5b1011055d170fc18a05ba048979d2089d1695 -j24 --abbreviate-paths -d0 --debug-configuration --build-dir="/home/uqhjung3/.conan/data/boost/1.78.0/_/_/build/cf5b1011055d170fc18a05ba048979d2089d1695"
b2: /lib64/libstdc++.so.6: version `GLIBCXX_3.4.21' not found (required by b2)
b2: /lib64/libstdc++.so.6: version `GLIBCXX_3.4.20' not found (required by b2)
boost/1.78.0:
boost/1.78.0: ERROR: Package 'cf5b1011055d170fc18a05ba048979d2089d1695' build failed

From the logs it looks like your compiler toolchain is quite old (GCC 4.8 was released ~2015) and the specific error at the end with b2 is related to libstdc++ not containing newer versions.

Can I ask what your platform/OS (and versions) are and if you have the most up to date compiler available?

If you have support for a package manager, you might want to try the instructions for building against OS packages here: https://github.com/nanoporetech/pod5-file-format#developing

If you can get me more info on your system, I can attempt to work on a solution - perhaps we can remove our boost dependency, if it is impossible to build on your platform.

Thanks,
George

[OZTaekOppa]

Hi George,

Thank you for your reply.
I will try again with a conda environment (using the latest GCC).

Regards,

Taek

[OZTaekOppa]

Unfortunately, there was no luck. Please see the attached file.

Pod5_Issue2.txt

And, my Univ. HPC is not allowed to use "sudo" command.
Here is the link (https://rcc.uq.edu.au/flashlite).

Cheers,

[0x55555555]

Hi @OZTaekOppa ,

If you have a newer version of GCC on the box, you can invoke conan specifically with that compiler:

> conan install --build=missing -s build_type=Release -s compiler=gcc -s compiler.version=10 ..

That should cause conan to select the newer compiler - you may also need to set CC/CXX variables to get conan to select the right compilers.

Thanks,

• George

[0x55555555]

Hi @OZTaekOppa ,

The latest release 0.0.17 does not require a binary build of boost - so should resolve your issue, can you have another go and let us know?

• George

[OZTaekOppa]

Hi George,
Sorry for the late reply.
Now, it is working fine including the installation.
Thank you so much!
Taek

[asan-emirsaleh]

Hi all!
@OZTaekOppa how did you fix the issue? Did you installed it inside conda environment? What packages also was bandled within it?