can not use HDF5. error with libblosc #234

xiuliren · 2015-05-09T20:52:40Z

ubuntu 14.04, julia V0.3

julia> using HDF5
Warning: error initializing module Blosc:
ErrorException("error compiling init: could not load module /usr/people/jingpeng/.julia/v0.3/Blosc/src/../deps/libblosc: /usr/people/jingpeng/.julia/v0.3/Blosc/src/../deps/libblosc: cannot open shared object file: No such file or directory")

ERROR: error compiling blosc_filter: could not load module /usr/people/jingpeng/.julia/v0.3/Blosc/src/../deps/libblosc: /usr/people/jingpeng/.julia/v0.3/Blosc/src/../deps/libblosc: cannot open shared object file: No such file or directory
in register_blosc at /usr/people/jingpeng/.julia/v0.3/HDF5/src/blosc_filter.jl:123
in include at ./boot.jl:245
in include_from_node1 at ./loading.jl:128
in include at ./boot.jl:245
in include_from_node1 at ./loading.jl:128
in reload_path at loading.jl:152
in _require at loading.jl:67
in require at loading.jl:51
while loading /usr/people/jingpeng/.julia/v0.3/HDF5/src/plain.jl, in expression starting on line 510
while loading /usr/people/jingpeng/.julia/v0.3/HDF5/src/HDF5.jl, in expression starting on line 1

rened · 2015-05-10T19:57:18Z

Can you try to run Pkg.build("Blosc") and see whether that succeeds?

xiuliren · 2015-05-12T18:56:20Z

thanks for the reply.
It seems that it is a bug of Blosc. I can not build Blosc.

julia> Pkg.build("Blosc")
INFO: Building Blosc
% Total % Received % Xferd Average Speed Time Time Time
Current
Dload Upload Total Spent Left
Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:--
--:--:-- 0curl: (77) error setting certificate verify locations:
CAfile: /etc/pki/tls/certs/ca-bundle.crt
CApath: none
===========================================================================================================[
ERROR: Blosc
]============================================================================================================

failed process: Process(curl -f -o c-blosc-1.5.0.tar.gz -L https://github.com/Blosc/c-blosc/archive/v1.5.0.tar.gz, ProcessExited(77))
[77]
while loading /usr/people/jingpeng/.julia/v0.3/Blosc/deps/build.jl, in
expression starting on line 17

===========================================================================================================[
BUILD ERRORS
]============================================================================================================

WARNING: Blosc had build errors.

packages with build errors remain installed in
/usr/people/jingpeng/.julia/v0.3
build the package(s) and all dependencies with Pkg.build("Blosc")
build a single package by running its deps/build.jl script

On Sun, May 10, 2015 at 3:57 PM, rened notifications@github.com wrote:

Can you try to run Pkg.build("Blosc") and see whether that succeeds?

—
Reply to this email directly or view it on GitHub
#234 (comment).

xiuliren · 2015-05-12T18:58:05Z

$ julia build.jl
% Total % Received % Xferd Average Speed Time Time Time
Current
Dload Upload Total Spent Left
Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:--
--:--:-- 0curl: (77) error setting certificate verify locations:
CAfile: /etc/pki/tls/certs/ca-bundle.crt
CApath: none
ERROR: failed process: Process(curl -f -o c-blosc-1.5.0.tar.gz -L https://github.com/Blosc/c-blosc/archive/v1.5.0.tar.gz, ProcessExited(77))
[77]
in pipeline_error at process.jl:502
in run at ./process.jl:479
in include at ./boot.jl:245
in include_from_node1 at loading.jl:128
in process_options at ./client.jl:285
in _start at ./client.jl:354
while loading /usr/people/jingpeng/.julia/v0.3/Blosc/deps/build.jl, in
expression starting on line 17

On Tue, May 12, 2015 at 2:55 PM, Jingpeng Wu jingpeng@princeton.edu wrote:

thanks for the reply.
It seems that it is a bug of Blosc. I can not build Blosc.

julia> Pkg.build("Blosc")
INFO: Building Blosc
% Total % Received % Xferd Average Speed Time Time Time
Current
Dload Upload Total Spent Left
Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:--
--:--:-- 0curl: (77) error setting certificate verify locations:
CAfile: /etc/pki/tls/certs/ca-bundle.crt
CApath: none
===========================================================================================================[
ERROR: Blosc
]============================================================================================================

failed process: Process(curl -f -o c-blosc-1.5.0.tar.gz -L https://github.com/Blosc/c-blosc/archive/v1.5.0.tar.gz
https://github.com/Blosc/c-blosc/archive/v1.5.0.tar.gz,
ProcessExited(77)) [77]
while loading /usr/people/jingpeng/.julia/v0.3/Blosc/deps/build.jl, in
expression starting on line 17

===========================================================================================================[
BUILD ERRORS
]============================================================================================================

WARNING: Blosc had build errors.

packages with build errors remain installed in
/usr/people/jingpeng/.julia/v0.3

build the package(s) and all dependencies with Pkg.build("Blosc")

build a single package by running its deps/build.jl script

On Sun, May 10, 2015 at 3:57 PM, rened notifications@github.com wrote:

Can you try to run Pkg.build("Blosc") and see whether that succeeds?

—
Reply to this email directly or view it on GitHub
#234 (comment).

stevengj · 2015-05-12T20:09:48Z

The curl command to download Blosc is failing. Are you behind a firewall or something?

rened · 2015-05-12T20:10:32Z

Could you please try to run Pkg.update() and then try again with Pkg.build("Blosc") - the URL does not exist any more (404).

simonster · 2015-05-12T20:17:39Z

@rened The URL https://github.com/Blosc/c-blosc/archive/v1.5.0.tar.gz exists, but it's getting auto-linked with the final backtick.

Based on the error, it looks like the problem is that curl on your system is misconfigured. Something is wrong with the CA bundle, so curl refuses to use SSL because it can't authenticate the connection. Does /etc/pki/tls/certs/ca-bundle.crt exist on your system? If not, you (or your system administrator) will need to figure out how to install the CA bundle so that curl can find it.

xiuliren · 2015-05-12T20:18:19Z

Yes, I am in princeton university, which probably have a firewall. However,
I have not find other links that I can not access.

I tried again, it failed.
Actually, my laptop have a working julia HDF5, which was build outside the
university!

julia> Pkg.update()
INFO: Updating METADATA...
INFO: Updating cache of Docile...
INFO: Updating cache of Compose...
INFO: Updating cache of HDF5...
INFO: Updating cache of Gadfly...
INFO: Computing changes...
INFO: Upgrading Compose: v0.3.11 => v0.3.12
INFO: Upgrading Docile: v0.4.12 => v0.4.13
INFO: Upgrading Gadfly: v0.3.11 => v0.3.12
INFO: Upgrading HDF5: v0.4.15 => v0.4.16
INFO: Building Blosc
% Total % Received % Xferd Average Speed Time Time Time
Current
Dload Upload Total Spent Left
Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:--
--:--:-- 0curl: (77) error setting certificate verify locations:
CAfile: /etc/pki/tls/certs/ca-bundle.crt
CApath: none
===========================================================================================================[
ERROR: Blosc
]============================================================================================================

failed process: Process(curl -f -o c-blosc-1.5.0.tar.gz -L https://github.com/Blosc/c-blosc/archive/v1.5.0.tar.gz, ProcessExited(77))
[77]
while loading /usr/people/jingpeng/.julia/v0.3/Blosc/deps/build.jl, in
expression starting on line 17

INFO: Building HDF5

===========================================================================================================[
BUILD ERRORS
]============================================================================================================

WARNING: Blosc had build errors.

packages with build errors remain installed in
/usr/people/jingpeng/.julia/v0.3
build the package(s) and all dependencies with Pkg.build("Blosc")
build a single package by running its deps/build.jl script

julia> Pkg.build("Blosc")
INFO: Building Blosc
% Total % Received % Xferd Average Speed Time Time Time
Current
Dload Upload Total Spent Left
Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:--
--:--:-- 0curl: (77) error setting certificate verify locations:
CAfile: /etc/pki/tls/certs/ca-bundle.crt
CApath: none
===============================================================================================================[
ERROR: Blosc
]================================================================================================================

failed process: Process(curl -f -o c-blosc-1.5.0.tar.gz -L https://github.com/Blosc/c-blosc/archive/v1.5.0.tar.gz, ProcessExited(77))
[77]
while loading /usr/people/jingpeng/.julia/v0.3/Blosc/deps/build.jl, in
expression starting on line 17

===============================================================================================================[
BUILD ERRORS
]================================================================================================================

WARNING: Blosc had build errors.

packages with build errors remain installed in
/usr/people/jingpeng/.julia/v0.3
build the package(s) and all dependencies with Pkg.build("Blosc")
build a single package by running its deps/build.jl script

On Tue, May 12, 2015 at 4:10 PM, rened notifications@github.com wrote:

Could you please try to run Pkg.update() and then try again with
Pkg.build("Blosc") - the URL does not exist any more (404).

—
Reply to this email directly or view it on GitHub
#234 (comment).

rened · 2015-05-12T20:21:01Z

@simonster ah, you are right of course... I first went after the CA issue, then thought it was just the URL...

xiuliren · 2015-05-18T19:46:05Z

I have fixed it by modifying the BinDeps.jl !

I add a "-k" option for curl.

return curl -f -k -o $filename -L $url

than I rebuild the Blosc

julia> Pkg.build("Blosc")
INFO: Building Blosc
% Total % Received % Xferd Average Speed Time Time Time
Current
Dload Upload Total Spent Left
Speed
100 121 0 121 0 0 1503 0 --:--:-- --:--:-- --:--:--
1920
100 233k 100 233k 0 0 903k 0 --:--:-- --:--:-- --:--:--
2290k
Compiling libblosc...
CC blosc.c
CC blosclz.c
CC shuffle.c
LINK libblosc

On Tue, May 12, 2015 at 4:21 PM, rened notifications@github.com wrote:

@simonster https://github.com/simonster ah, you are right of course...
I first went after the CA issue, then thought it was just the URL...

—
Reply to this email directly or view it on GitHub
#234 (comment).

bjarthur · 2015-06-18T21:08:11Z

i had similar problems that were fixed by nuking ~/.julia/v0.3

stevengj · 2015-06-24T18:16:56Z

Should there be a BinDeps issue to add a way to use curl -k? i.e. make download_cmd(url::String, filename::String) take an optional insecure::Bool=false argument?

ewiger · 2015-06-25T20:47:35Z

Solution is to tell your curl where to find CA bundle:

# fix CURL certificates path
export CURL_CA_BUNDLE=/etc/ssl/certs/ca-certificates.crt

http://stackoverflow.com/questions/3160909/how-do-i-deal-with-certificates-using-curl-while-trying-to-access-an-https-url/31060428#31060428

musm · 2019-07-06T04:36:10Z

Stale issue. Post back if still a problem.

stevengj mentioned this issue Jul 21, 2015

Building issues Win64 JuliaIO/Blosc.jl#10

Closed

zhenpan mentioned this issue Jun 5, 2016

Failure to install packages with "sudo: no tty present and no askpass program specified" error JuliaPackaging/BinDeps.jl#199

Open

timbitz mentioned this issue Jul 6, 2017

Cannot build whippet... timbitz/Whippet.jl#49

Closed

musm closed this as completed Jul 6, 2019

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can not use HDF5. error with libblosc #234

can not use HDF5. error with libblosc #234

xiuliren commented May 9, 2015

rened commented May 10, 2015

xiuliren commented May 12, 2015

xiuliren commented May 12, 2015

stevengj commented May 12, 2015

rened commented May 12, 2015

simonster commented May 12, 2015

xiuliren commented May 12, 2015

rened commented May 12, 2015

xiuliren commented May 18, 2015

bjarthur commented Jun 18, 2015

stevengj commented Jun 24, 2015

ewiger commented Jun 25, 2015

musm commented Jul 6, 2019

can not use HDF5. error with libblosc #234

can not use HDF5. error with libblosc #234

Comments

xiuliren commented May 9, 2015

rened commented May 10, 2015

xiuliren commented May 12, 2015

xiuliren commented May 12, 2015

stevengj commented May 12, 2015

rened commented May 12, 2015

simonster commented May 12, 2015

xiuliren commented May 12, 2015

rened commented May 12, 2015

xiuliren commented May 18, 2015

bjarthur commented Jun 18, 2015

stevengj commented Jun 24, 2015

ewiger commented Jun 25, 2015

musm commented Jul 6, 2019