Julia: "error initializing LibGit2 module" when CA certificates not found

Created on 27 Sep 2016 · 74Comments · Source: JuliaLang/julia

Using openSUSE Leap 42.1:
24 hours ago a git pull followed by a make && make testall ran fine. This morning I had an error in make:

...
patching file tests/online/badssl.c
CMake Error: The current CMakeCache.txt directory /home/colin/Downloads/julia6/deps/scratch/libgit2-211e117a0590583a720c53172406f34186c543bd/CMakeCache.txt is different than the directory /home/colin/Downloads/julia/deps/scratch/libgit2-211e117a0590583a720c53172406f34186c543bd where CMakeCache.txt was created. This may result in binaries being created in the wrong place. If you are not sure, reedit the CMakeCache.txt
CMake Error: The source "/home/colin/Downloads/julia6/deps/srccache/libgit2-211e117a0590583a720c53172406f34186c543bd/CMakeLists.txt" does not match the source "/home/colin/Downloads/julia/deps/srccache/libgit2-211e117a0590583a720c53172406f34186c543bd/CMakeLists.txt" used to generate cache.  Re-run cmake with a different source directory.
/home/colin/Downloads/julia6/deps/libgit2.mk:66: recipe for target 'scratch/libgit2-211e117a0590583a720c53172406f34186c543bd/build-configured' failed
make[1]: *** [scratch/libgit2-211e117a0590583a720c53172406f34186c543bd/build-configured] Error 1
Makefile:81: recipe for target 'julia-deps' failed
make: *** [julia-deps] Error 2

I thought I had fixed this with make -C deps distclean-libgit2 distclean-mbedtls distclean-libssh2 which allowed make to run to the end. However now Julia 0.6 fails to launch with:

> julia6
fatal: error thrown and no exception handler available.
Base.InitError(mod=:LibGit2, error=ErrorException("error initializing LibGit2 module"))
rec_backtrace at /home/colin/Downloads/julia6/src/stackwalk.c:84
record_backtrace at /home/colin/Downloads/julia6/src/task.c:238
jl_throw at /home/colin/Downloads/julia6/src/task.c:560
__init__ at ./libgit2/libgit2.jl:539
unknown function (ip: 0x7f60d03e3e08)
jl_call_method_internal at /home/colin/Downloads/julia6/src/julia_internal.h:218 [inlined]
jl_apply_generic at /home/colin/Downloads/julia6/src/gf.c:1852
jl_apply at /home/colin/Downloads/julia6/src/julia.h:1376 [inlined]
jl_module_run_initializer at /home/colin/Downloads/julia6/src/toplevel.c:83
_julia_init at /home/colin/Downloads/julia6/src/init.c:702
julia_init at /home/colin/Downloads/julia6/src/task.c:289
unknown function (ip: 0x4014cd)
__libc_start_main at /lib64/libc.so.6 (unknown line)
unknown function (ip: 0x40151f)

Prebuilt Julia 0.5 works fine.

libgit2 linux regression

Source

colbec

Most helpful comment

I'm having the same problem on Ubuntu (on Windows!) with a source build. The fix for SSL_CERT_FILE works to launch Julia but I cannot initialize the package repository - cloning METADATA fails with a certificate error.

kshyatt on 6 Oct 2016

👍2

All 74 comments

What does ldd usr/lib/libgit2.so say?

tkelman on 27 Sep 2016

If you see anything in there about libssl or libcrypto (but not of the mbed variety), try make cleanall && make

tkelman on 27 Sep 2016

One curiosity is that if I do a find ./ -name libgit2.so from julia main directory I find eight different files matched, some clearly symlinks, but others may be different residual versions causing confusion.

> ldd usr/lib/libgit2.so
    linux-vdso.so.1 (0x00007ffeced63000)
    libcurl.so.4 => /home/colin/Downloads/julia6/usr/lib/libcurl.so.4 (0x00007f5926bf8000)
    libz.so.1 => /lib64/libz.so.1 (0x00007f59269b2000)
    libmbedtls.so.10 => /home/colin/Downloads/julia6/usr/lib/libmbedtls.so.10 (0x00007f592678b000)
    libmbedx509.so.0 => /home/colin/Downloads/julia6/usr/lib/libmbedx509.so.0 (0x00007f5926577000)
    libmbedcrypto.so.0 => /home/colin/Downloads/julia6/usr/lib/libmbedcrypto.so.0 (0x00007f5926323000)
    libssh2.so.1 => /home/colin/Downloads/julia6/usr/lib/libssh2.so.1 (0x00007f59260f0000)
    librt.so.1 => /lib64/librt.so.1 (0x00007f5925ee8000)
    libpthread.so.0 => /lib64/libpthread.so.0 (0x00007f5925cca000)
    libc.so.6 => /lib64/libc.so.6 (0x00007f5925922000)
    /lib64/ld-linux-x86-64.so.2 (0x00005572745ee000)

Then:
make cleanall is successful, but make finishes with:

...
configure: creating ./config.status
config.status: creating libuv.pc
config.status: creating Makefile
config.status: executing depfiles commands
config.status: executing libtool commands
make[2]: *** No rule to make target '/home/colin/Downloads/julia/deps/srccache/libuv-8d5131b6c1595920dd30644cd1435b4f344b46c8/src/fs-poll.c', needed by 'src/libuv_la-fs-poll.lo'.  Stop.
/home/colin/Downloads/julia6/deps/libuv.mk:37: recipe for target 'scratch/libuv-8d5131b6c1595920dd30644cd1435b4f344b46c8/build-compiled' failed
make[1]: *** [scratch/libuv-8d5131b6c1595920dd30644cd1435b4f344b46c8/build-compiled] Error 2
Makefile:81: recipe for target 'julia-deps' failed
make: *** [julia-deps] Error 2

colbec on 27 Sep 2016

I'm not sure what to make of the libuv failure. Does it persist after make -C deps distclean-libuv ?

tkelman on 27 Sep 2016

Can you also check ldd on some of the other libraries, libcurl, libssh2, and the libmbed* ? Is anything obviously missing?

tkelman on 27 Sep 2016

After make -C deps distclean-libuv make still failing.

> make
 cd /home/colin/Downloads/julia/deps/srccache/libunwind-1.1-julia2 && /bin/sh /home/colin/Downloads/julia/deps/srccache/libunwind-1.1-julia2/config/missing automake-1.15 --gnu Makefile
/bin/sh: line 10: cd: /home/colin/Downloads/julia/deps/srccache/libunwind-1.1-julia2: No such file or directory
Makefile:477: recipe for target '/home/colin/Downloads/julia/deps/srccache/libunwind-1.1-julia2/Makefile.in' failed
make[2]: *** [/home/colin/Downloads/julia/deps/srccache/libunwind-1.1-julia2/Makefile.in] Error 1
/home/colin/Downloads/julia6/deps/unwind.mk:31: recipe for target '/home/colin/Downloads/julia6/usr-staging/libunwind-1.1-julia2.tgz' failed
make[1]: *** [/home/colin/Downloads/julia6/usr-staging/libunwind-1.1-julia2.tgz] Error 2
Makefile:81: recipe for target 'julia-deps' failed
make: *** [julia-deps] Error 2

colbec on 27 Sep 2016

Something is very wrong, but I'm not sure if it's in Julia's makefiles or local to your particular clone. Does a build from scratch work correctly (maybe in a new clone to at least keep this build's copies of llvm and openblas around if they're still working)?

tkelman on 27 Sep 2016

The directory usr/lib does not contain a libcurl,so or libssh2.so or libmbed*.so. Should they be there? Doing a find for libcurl.so finds them in .deps/build and scratch.

I will wipe the cache and try again.

colbec on 27 Sep 2016

@tkelman Just finished a re-clone (everything deleted and recreated from scratch) of latest v 0.6 dev, and make is successful but again, will not launch as above.

colbec on 27 Sep 2016

I just hit this on power:

    JULIA test/all
fatal: error thrown and no exception handler available.
Base.InitError(mod=:LibGit2, error=ErrorException("error initializing LibGit2 module"))
rec_backtrace at /home/valentin/juliatest/src/stackwalk.c:84
record_backtrace at /home/valentin/juliatest/src/task.c:238
jl_throw at /home/valentin/juliatest/src/task.c:560
__init__ at ./libgit2/libgit2.jl:539
unknown function (ip: 0x3fffa68cf1bf)
jl_call_method_internal at /home/valentin/juliatest/src/julia_internal.h:239 [inlined]
jl_apply_generic at /home/valentin/juliatest/src/gf.c:1852
jl_apply at /home/valentin/juliatest/src/julia.h:1376 [inlined]
jl_module_run_initializer at /home/valentin/juliatest/src/toplevel.c:83
_julia_init at /home/valentin/juliatest/src/init.c:702
julia_init at /home/valentin/juliatest/src/task.c:289
main at /home/valentin/juliatest/ui/repl.c:247
unknown function (ip: 0x3fffb226457f)
__libc_start_main at /lib64/power8/libc.so.6 (unknown line)
make: *** [all] Error 1
make: Leaving directory `/home/valentin/juliatest/test'

vchuravy on 27 Sep 2016

Same here, Arch Linux x86-64, both libgit2 and libssh2 are properly linked to mbedtls. Seems like git_mbedtls_stream_global_init is returning -1.

maleadt on 27 Sep 2016

It isn't finding the CA certificates, after trying:

ENV[X509_CERT_FILE_EVP="SSL_CERT_FILE"]
ENV[X509_CERT_DIR_EVP="SSL_CERT_DIR"]
"/usr/lib/ssl/cert.pem"
"/usr/lib/ssl/certs"

In other words, this is failing.

EDIT: on my Debian systems, "/usr/lib/ssl/certs" symlinks to "/etc/ssl/certs", but on Arch this is not the case. Maybe we should add "/etc/ssl/certs" to the search path? As a workaround, exporting SSL_CERT_DIR makes Julia work again.

maleadt on 27 Sep 2016

❤1

On the my redhat machine at hand I have to use SSL_CERT_FILE=/etc/pki/tls/cert.pem or SSL_CERT_FILE=/etc/pki/tls/certs/ca-bundle.crt

https://www.happyassassin.net/2015/01/12/a-note-about-ssltls-trusted-certificate-stores-and-platforms/

vchuravy on 27 Sep 2016

Looks like we need a few non-debian-shaped defaults too for the cert locations. There's something in make install or make binary-dist that copies certs around, things might work after that step runs. If so we could move it earlier.

tkelman on 27 Sep 2016

On openSUSE Leap 42.1 SSL_CERT_FILE=/etc/ssl/certs/certSIGN_ROOT_CA.pem allows v0.6-dev to launch correctly. Not sure if this is the right .pem to use, just chose the closest to alternatives found above. Thanks.

Edit: I guess it is not the correct .pem. Pkg.update() immediately complains the certificate is wrong.

Edit 2: SSL_CERT_FILE=/var/lib/ca-certificates/ca-bundle.pem gets things working again. The alternate setting of SSL_CERT_DIR suggested above does not work on openSUSE.

colbec on 27 Sep 2016

👍1

We should also really try to make the error message clearer here if we can.

tkelman on 27 Sep 2016

I think I hit this error on Ubuntu, so it applies to Debian-based distros too:

fatal: error thrown and no exception handler available.
Base.InitError(mod=:LibGit2, error=ErrorException("error initializing LibGit2 module"))
rec_backtrace at /home/fengyang/julia/src/stackwalk.c:84
record_backtrace at /home/fengyang/julia/src/task.c:238
jl_throw at /home/fengyang/julia/src/task.c:560
__init__ at ./libgit2/libgit2.jl:539
unknown function (ip: 0x7fdc8d179f38)
jl_call_method_internal at /home/fengyang/julia/src/julia_internal.h:239 [inlined]
jl_apply_generic at /home/fengyang/julia/src/gf.c:1852
jl_apply at /home/fengyang/julia/src/julia.h:1377 [inlined]
jl_module_run_initializer at /home/fengyang/julia/src/toplevel.c:83
_julia_init at /home/fengyang/julia/src/init.c:702
julia_init at /home/fengyang/julia/src/task.c:289
main at /home/fengyang/julia/ui/repl.c:247
__libc_start_main at /build/glibc-GKVZIf/glibc-2.23/csu/../csu/libc-start.c:291
unknown function (ip: 0x401438)

Setting the SSL_CERT_FILE to /usr/lib/ssl/certs/ca-certificates.crt and SSL_CERT_DIR to /usr/lib/ssl/certs repaired the issue.

TotalVerb on 29 Sep 2016

It may also depend on which particular ca-certificates package sets you have installed, since those come in a few different variants.

tkelman on 29 Sep 2016

Same problem on Fedora 24.

$ ./julia
fatal: error thrown and no exception handler available.
Base.InitError(mod=:LibGit2, error=ErrorException("error initializing LibGit2 module"))
rec_backtrace at /home/rick/src/julia/julia/src/stackwalk.c:84
record_backtrace at /home/rick/src/julia/julia/src/task.c:238
jl_throw at /home/rick/src/julia/julia/src/task.c:560
__init__ at ./libgit2/libgit2.jl:539
unknown function (ip: 0x7fb07647cf08)
jl_call_method_internal at /home/rick/src/julia/julia/src/julia_internal.h:239 [inlined]
jl_apply_generic at /home/rick/src/julia/julia/src/gf.c:1852
jl_apply at /home/rick/src/julia/julia/src/julia.h:1377 [inlined]
jl_module_run_initializer at /home/rick/src/julia/julia/src/toplevel.c:83
_julia_init at /home/rick/src/julia/julia/src/init.c:702
julia_init at /home/rick/src/julia/julia/src/task.c:289
main at /home/rick/src/julia/julia/ui/repl.c:247
__libc_start_main at /lib64/libc.so.6 (unknown line)
unknown function (ip: 0x4013c8)

rickhg12hs on 29 Sep 2016

👍1

We'll have to find where the default cert search path is set and add more. Someone who has a source build in one of the problematic configurations will be best placed to test proposed additions.

tkelman on 29 Sep 2016

The patch we are carrying against mbedtls is setting these defaults. https://github.com/JuliaLang/julia/blob/f241e23db214f008baef80bf6bcf75a6c7efe5f9/deps/patches/libgit2-mbedtls.patch#L295

vchuravy on 29 Sep 2016

It honors SSL_CERT_DIR and SSL_CERT_FILE though. If those aren't set, perhaps we should do some searching. Kind of unfortunate that this initialization is happening eagerly though, would be better for startup time if we could defer it until an https connection is first initiated.

tkelman on 29 Sep 2016

We also have some code here https://github.com/JuliaLang/julia/blob/b36141f4799d73113b3597ee94d5925929b2ccd5/Makefile#L456-L459 that runs during make binary-dist to copy the build system's certs into the binary-dist tarball. If that snippet works more broadly, we could move it into deps/libgit2.mk and have it always run?

tkelman on 29 Sep 2016

At least on Linux the system's certs are meant to be upgraded over-time and
this would mean that the certs could get outdated.
It is quite sad that these locations are so non-standard. In my opinion the
correct course of action is to extend the lists of plausible defaults
(right now we are looking into a Debian specific place) and make libgit
init lazy.

On Fri, 30 Sep 2016 at 05:53 Tony Kelman [email protected] wrote:

We also have some code here
https://github.com/JuliaLang/julia/blob/b36141f4799d73113b3597ee94d5925929b2ccd5/Makefile#L456-L459
that runs during make binary-dist to copy the build system's certs into
the binary-dist tarball. If that snippet works more broadly, we could move
that code snippet into deps/libgit2.mk and have it always run?

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vchuravy on 29 Sep 2016

I'd rather have outdated certs than binaries that don't work standalone in minimal environments.

tkelman on 29 Sep 2016

I don't dispute that for binaries that we distribute, but it is not a
solution for people that build ourselves or binaries that people get
through their package manager.

On Fri, 30 Sep 2016 at 06:15 Tony Kelman [email protected] wrote:

I'd rather have outdated certs than binaries that don't work standalone in
minimal environments.

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vchuravy on 29 Sep 2016

Why isn't it a solution for source builds? It's asking system-installed software where it decided to put things, and copying them to a known location used as a fallback when hard-coded paths all fail. We can work out the makefile rules to have the timestamps auto-update the copy if system certs get updated if you're worried about a source build sitting around for that long without having make cleanall called on it.

tkelman on 29 Sep 2016

I can confirm that on Fedora 24

$ export SSL_CERT_FILE=/etc/pki/tls/cert.pem

Allowed Julia to launch normally and Pkg.update() succeeded as well.

rickhg12hs on 3 Oct 2016

👍2

This worked for me on RHEL7.
export SSL_CERT_FILE=/etc/pki/tls/certs/ca-bundle.crt

sfishback on 5 Oct 2016

Should clarify, for RHEL7 both of these point to /etc/pki/ca-trust/extracted/pem/tls-ca-bundle.pem
I modified to avoid the extra symbolic link hop.
export SSL_CERT_FILE=/etc/pki/ca-trust/extracted/pem/tls-ca-bundle.pem

$ ls -l /etc/pki/tls/certs/ca-bundle.crt
lrwxrwxrwx. 1 root root 49 Apr 14 17:20 /etc/pki/tls/certs/ca-bundle.crt -> /etc/pki/ca-trust/extracted/pem/tls-ca-bundle.pem

$ ls -l /etc/pki/tls/cert.pem
lrwxrwxrwx. 1 root root 49 Apr 14 17:20 /etc/pki/tls/cert.pem -> /etc/pki/ca-trust/extracted/pem/tls-ca-bundle.pem

sfishback on 5 Oct 2016

kshyatt on 6 Oct 2016

👍2

I'm seeing the same problem as @kshyatt here on Ubuntu on Windows. I just installed Bash for Windows yesterday, so this is a clean install that I'm seeing this on.

davidanthoff on 12 Oct 2016

I think I found the root problem: https://github.com/libgit2/libgit2/pull/3935#issuecomment-253910017

The current workaround is to have Julia set SSL_CERT_FILE manually during libgit2 initialization. See https://github.com/JuliaLang/julia/pull/18936 for the important bits, I'm not opening a PR yet, because I'm waiting for a response on the libgit2 PR I commented on.

staticfloat on 14 Oct 2016

should be fixed by https://github.com/JuliaLang/julia/pull/18936. report back if not.

tkelman on 16 Oct 2016

Hmmm.... Still failing on openSUSE Leap 42.1 after git pull to latest Julia.
As before, export SSL_CERT_FILE=/etc/ssl/ca-bundle.pem added to .profile fixes the problem.
Tried make -C deps distclean-libgit2 distclean-mbedtls distclean-libssh2 and make was successful but still cannot start Julia 0.6 without the profile fix.

colbec on 16 Oct 2016

how about after make cleanall ?

tkelman on 16 Oct 2016

Still fails.

colbec on 16 Oct 2016

This fixed the problem on Fedora 24 at least.

nalimilan on 16 Oct 2016

what does openssl version -d return?

tkelman on 16 Oct 2016

openssl version -d
OPENSSLDIR: "/etc/ssl"

colbec on 16 Oct 2016

Oh, looks like opensuse calls it ca-bundle.pem instead of cert.pem. We could probably add a second fallback to check that name. Which ca-certificates packages do you have installed? cert.pem might be in ca-certificates-mozilla instead of just ca-certificates? I think I had seen git or some other programs fail to work over https unless ca-certificates-mozilla is installed.

tkelman on 17 Oct 2016

Also still fails on Bash on Ubuntu for Windows. openssl version -d returns OPENSSLDIR: "/usr/lib/ssl".

davidanthoff on 17 Oct 2016

This is all hidden inside ifdefs for Linux, do we need to do this for
Windows as well?

On Sun, Oct 16, 2016, 22:05 David Anthoff [email protected] wrote:

Also still fails on Bash on Ubuntu for Windows. openssl version -d
returns OPENSSLDIR: "/usr/lib/ssl".

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staticfloat on 17 Oct 2016

I don't think so, Bash on Windows should just be Ubuntu, as far as I understand it...

davidanthoff on 17 Oct 2016

This is what I get as the Ubuntu version:

davidanthoff@DANTHOFF-HOME:~/source/julia$ lsb_release -a
No LSB modules are available.
Distributor ID: Ubuntu
Description:    Ubuntu 14.04.5 LTS
Release:        14.04
Codename:       trusty
davidanthoff@DANTHOFF-HOME:~/source/julia$

davidanthoff on 17 Oct 2016

@tkelman A system-wide search for "cert.pem" on openSUSE produces only two files, both in julia-related, not system, locations. A search for "certs.pem" finds no files with that name.
Searching for "ca-certificates*" finds

/usr/lib/ca-certificates
/usr/share/doc/packages/ca-certificates-mozilla
/usr/share/doc/packages/ca-certificates
/var/lib/ca-certificates

and digging into that /usr/share mozilla directory shows it contains one single file COPYING with license information.

/etc/ssl has 4 entries,

lrwxrwxrwx 1 root root    38 Oct 29  2015 ca-bundle.pem -> /var/lib/ca-certificates/ca-bundle.pem
lrwxrwxrwx 1 root root    28 Oct 29  2015 certs -> /var/lib/ca-certificates/pem
-rw-r--r-- 1 root root 10835 Sep 27 11:52 openssl.cnf
drwx------ 1 root root     0 Sep 27 11:52 private

And the only reference to "_certificates-mozilla_" is the /usr/share thing above.

colbec on 17 Oct 2016

Alright, I think I've got a PR that should work on everybody's system. There are a few different naming conventions, but we'll just need to add more to the list as new systems find brave and exciting ways to name the same file.

staticfloat on 18 Oct 2016

Julia 0.6 is now working again on openSUSE Leap 42.1 without specification of $SSL_CERT_FILE as of

Version 0.6.0-dev.1031 (2016-10-19 02:14 UTC)
Commit 90a3740 (0 days old master)
x86_64-suse-linux

colbec on 19 Oct 2016

Thanks so much for testing @colbec! Are you able to install (setting JULIA_PKGDIR to something temporary may be useful for testing) packages that separately download source files, such as Blosc.jl?

tkelman on 19 Oct 2016

@tkelman I added and tested Blosc.jl and FYI it runs fine on Julia 0.6 on openSUSE. It's not on my list of packages regularly in use so the testing will not be regular or adventurous. I am of course open to specific requests.

colbec on 20 Oct 2016

thanks @colbec. let's call this mostly fixed, but may need to add more cert paths for additional distros

tkelman on 21 Oct 2016

Is there a new issue for these additional cert paths? Thinks don't yet work for bash on windows, as far as I can tell...

davidanthoff on 21 Oct 2016

I'm getting this problem on Ubuntu again.

fengyang@serval ~/julia> make test
    JULIA test/all
fatal: error thrown and no exception handler available.
Base.InitError(mod=:LibGit2, error=ErrorException("error initializing LibGit2 module"))
rec_backtrace at /home/fengyang/julia/src/stackwalk.c:84
record_backtrace at /home/fengyang/julia/src/task.c:238
jl_throw at /home/fengyang/julia/src/task.c:560
__init__ at ./libgit2/libgit2.jl:558
unknown function (ip: 0x7fa1f2dc6c68)
jl_call_method_internal at /home/fengyang/julia/src/julia_internal.h:239 [inlined]
jl_apply_generic at /home/fengyang/julia/src/gf.c:1861
jl_apply at /home/fengyang/julia/src/julia.h:1378 [inlined]
jl_module_run_initializer at /home/fengyang/julia/src/toplevel.c:83
_julia_init at /home/fengyang/julia/src/init.c:696
julia_init at /home/fengyang/julia/src/task.c:289
main at /home/fengyang/julia/ui/repl.c:247
__libc_start_main at /build/glibc-GKVZIf/glibc-2.23/csu/../csu/libc-start.c:291
unknown function (ip: 0x401438)
Makefile:19: recipe for target 'all' failed
make[1]: *** [all] Error 1
Makefile:556: recipe for target 'test' failed
make: *** [test] Error 2

Do I need to change certs again?

TotalVerb on 22 Nov 2016

The problem does not go away with make cleanall.

TotalVerb on 22 Nov 2016

which ubuntu version? may need more paths as in https://github.com/JuliaLang/julia/pull/18997/files#diff-a01ad0cac7aa5a648c5d00ec39bd9afc

tkelman on 23 Nov 2016

I've just updated and upgraded Ubuntu and I'm getting this problem on Windows 10 through the Windows Subsystem for Linux with the default julia installed with sudo apt install julia:

C:\Users\Ismael

λ bash
ismaelvc@TOYBOX /mnt/c/Users/Ismael % julia
fatal: error thrown and no exception handler available.
Base.InitError(mod=:LibGit2, error=ErrorException("error initializing LibGit2 module"))
rec_backtrace at /build/julia-mNkFS7/julia-0.6.0/src/stackwalk.c:84
record_backtrace at /build/julia-mNkFS7/julia-0.6.0/src/task.c:238
jl_throw at /build/julia-mNkFS7/julia-0.6.0/src/task.c:560
__init__ at ./libgit2/libgit2.jl:558
unknown function (ip: 0x7f6fb2c90928)
jl_call_method_internal at /build/julia-mNkFS7/julia-0.6.0/src/julia_internal.h:239 [inlined]
jl_apply_generic at /build/julia-mNkFS7/julia-0.6.0/src/gf.c:1861
jl_apply at /build/julia-mNkFS7/julia-0.6.0/src/julia.h:1378 [inlined]
jl_module_run_initializer at /build/julia-mNkFS7/julia-0.6.0/src/toplevel.c:83
_julia_init at /build/julia-mNkFS7/julia-0.6.0/src/init.c:696
julia_init at /build/julia-mNkFS7/julia-0.6.0/src/task.c:289
unknown function (ip: 0x40138d)
__libc_start_main at /build/eglibc-oGUzwX/eglibc-2.19/csu/libc-start.c:287
unknown function (ip: 0x4013df)

ismaelvc@TOYBOX /mnt/c/Users/Ismael % cat /etc/issue
Ubuntu 14.04.5 LTS \n \l

ismaelvc@TOYBOX /mnt/c/Users/Ismael % uname -a
Linux TOYBOX 3.4.0+ #1 PREEMPT Thu Aug 1 17:06:05 CST 2013 x86_64 x86_64 x86_64 GNU/Linux

ismaelvc@TOYBOX /mnt/c/Users/Ismael % lsb_release -a
No LSB modules are available.
Distributor ID: Ubuntu
Description:    Ubuntu 14.04.5 LTS
Release:        14.04
Codename:       trusty

ismaelvc@TOYBOX /mnt/c/Users/Ismael % exit

C:\Users\Ismael
λ ver

Microsoft Windows [Versión 10.0.14393]

SalchiPapa on 25 Nov 2016

@Ismael-VC Could you test https://github.com/JuliaLang/julia/pull/19390 and see if it resolves the issue?

TotalVerb on 25 Nov 2016

@TotalVerb I'm going to try to build Julia from source, using your fix if I get the same error while building, but the error I report above comes from the julia from the ubuntu package repositories, I think your fix doesn't work on that, since that julia is already built.

SalchiPapa on 25 Nov 2016

@Ismael-VC Now that is an install case I never thought of when making the Julia PPA.

What does openssl version -d say for you?

staticfloat on 25 Nov 2016

@staticfloat the output of that and also which and julia info:

ismaelvc@TOYBOX ~ % openssl version -d
OPENSSLDIR: "/usr/lib/ssl"

ismaelvc@TOYBOX ~ % which openssl
/usr/bin/openssl

ismaelvc@TOYBOX ~ % apt show julia
Package: julia
Priority: extra
Section: science
Installed-Size: 540 MB
Maintainer: Debian Julia Team <[email protected]>
Version: 0.6.0-3000~201611231441~ubuntu14.04.1
Suggests: ess (>= 12.09-1~), julia-doc
Depends: libc6 (>= 2.17), libgcc1 (>= 1:4.1.1), libgfortran3 (>= 4.6), liblapack3 | liblapack.so.3, libopenblas-base, libstdc++6 (>= 4.8), zlib1g (>= 1:1.2.0), liblapack3 | libatlas3-base, libfftw3-3, libcholmod1.7.1 | libcholmod2.1.2 | libcholmod3.0.6 | libcholmod3, libumfpack5.4.0 | libumfpack5.6.2 | libumfpack5.7.1 | libumfpack5, libgmp10 (>= 6.1.0), libarpack2, librmath-julia-dev, libmpfr4, git, libssl1.0.0
Pre-Depends: multiarch-support
Download-Size: 121 MB
APT-Manual-Installed: yes
APT-Sources: http://ppa.launchpad.net/staticfloat/julianightlies/ubuntu/ trusty/main amd64 Packages
Description: high-performance programming language for technical computing
 Julia is a high-level, high-performance dynamic programming language for
 technical computing, with syntax that is familiar to users of other technical
 computing environments. It provides a sophisticated compiler, distributed
 parallel execution, numerical accuracy, and an extensive mathematical function
 library. The library, mostly written in Julia itself, also integrates mature,
 best-of-breed C and Fortran libraries for linear algebra, random number
 generation, FFTs, and string processing. Julia programs are organized around
 defining functions, and overloading them for different combinations of
 argument types (which can also be user-defined).
 .
 This package provides a complete Julia installation (JIT compiler, standard
 library, text-based user interface).

N: There are 2 additional records. Please use the '-a' switch to see them.

SalchiPapa on 25 Nov 2016

Can you show me what files are sitting in /usr/lib/ssl? Specifically, I'm looking for something that looks like a bundle of SSL certificates, hopefully something named certs.pem or ca.crt or something like that.

staticfloat on 27 Nov 2016

It might also be named certs/ca-certificates.crt.

TotalVerb on 27 Nov 2016

@staticfloat here is what's in that path:

ismaelvc@TOYBOX ~ % tree /usr/lib/ssl
/usr/lib/ssl
├── certs -> /etc/ssl/certs
├── misc
│   ├── CA.pl
│   ├── CA.sh
│   ├── c_hash
│   ├── c_info
│   ├── c_issuer
│   ├── c_name
│   └── tsget
├── openssl.cnf -> /etc/ssl/openssl.cnf
└── private -> /etc/ssl/private

3 directories, 8 files

SalchiPapa on 27 Nov 2016

What's inside certs?

On Sat, Nov 26, 2016, 22:03 Ismael Venegas Castelló <
[email protected]> wrote:

@staticfloat https://github.com/staticfloat here is what's in that path:

ismaelvc@TOYBOX ~ % tree /usr/lib/ssl
/usr/lib/ssl
├── certs -> /etc/ssl/certs
├── misc
│ ├── CA.pl
│ ├── CA.sh
│ ├── c_hash
│ ├── c_info
│ ├── c_issuer
│ ├── c_name
│ └── tsget
├── openssl.cnf -> /etc/ssl/openssl.cnf
└── private -> /etc/ssl/private

3 directories, 8 files

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staticfloat on 27 Nov 2016

Lots of .pems I don't see anything with git:

ismaelvc@TOYBOX ~ % tree /usr/lib/ssl/certs | grep -i git     
1 ismaelvc@TOYBOX ~ %

https://gist.github.com/Ismael-VC/a8341a115139a6823946d9b6c0b2b517

SalchiPapa on 27 Nov 2016

Fengyang is right. It's called "certs/ca-certificates.crt". I believe there
is a PR open right now to fix this.

On Sat, Nov 26, 2016, 22:27 Ismael Venegas Castelló <
[email protected]> wrote:

Lots of .pems I don't see anything with git:

https://gist.github.com/Ismael-VC/a8341a115139a6823946d9b6c0b2b517

1 ismaelvc@TOYBOX ~ % tree /usr/lib/ssl/certs | grep -i git :( 1 ismaelvc@TOYBOX ~ %

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staticfloat on 27 Nov 2016

I'm getting the same error with the latest master, but setting SSL_CERT_DIR and SSL_CERT_FILE did not fix it:

creanj@mastermind:~/fasttmp/build/julia_0.6_2$ ./julia
fatal: error thrown and no exception handler available.
Base.InitError(mod=:LibGit2, error=ErrorException("error initializing LibGit2 module"))
rec_backtrace at /fasttmp/creanj/build/julia_0.6_2/src/stackwalk.c:84
record_backtrace at /fasttmp/creanj/build/julia_0.6_2/src/task.c:239
jl_throw at /fasttmp/creanj/build/julia_0.6_2/src/task.c:565
__init__ at ./libgit2/libgit2.jl:628
unknown function (ip: 0x7fe7e84e9698)
jl_call_method_internal at /fasttmp/creanj/build/julia_0.6_2/src/julia_internal.h:248 [inlined]
jl_apply_generic at /fasttmp/creanj/build/julia_0.6_2/src/gf.c:2217
jl_apply at /fasttmp/creanj/build/julia_0.6_2/src/julia.h:1410 [inlined]
jl_module_run_initializer at /fasttmp/creanj/build/julia_0.6_2/src/toplevel.c:85
_julia_init at /fasttmp/creanj/build/julia_0.6_2/src/init.c:704
julia_init at /fasttmp/creanj/build/julia_0.6_2/src/task.c:292
main at /fasttmp/creanj/build/julia_0.6_2/ui/repl.c:259
__libc_start_main at /home/aurel32/debian/co-packages/eglibc/squeeze/eglibc-2.11.3/csu/libc-start.c:244
unknown function (ip: 0x4016ac)

ca-certificates.crt is located in /etc/ssl/certs/, and /usr/lib/ssl/certs/ is a symlink to it.

JaredCrean2 on 25 Jan 2017

Please gist the output of strace ./julia.

staticfloat on 25 Jan 2017

Here it is.

JaredCrean2 on 25 Jan 2017

Not solved. On one of the clusters I use, I just got the error again and I can fix it with SSL_CERT_FILE=/etc/ssl/certs/certSIGN_ROOT_CA.pem. This is on master.

andreasnoack on 23 Mar 2017

What distribution is it? I've never seen one with a name so strange. Is that the cert file that gets used by openssl if you do an s_client test?

staticfloat on 23 Mar 2017

Anyone who still has an issue here, try writing a patch similar to https://github.com/JuliaLang/julia/pull/19390 adding a case for wherever your system has the certs, since almost everyone else is covered by the existing cases.

tkelman on 30 Mar 2017

I don't see this issue anymore

andreasnoack on 11 Oct 2017

I investigated this further and think there is a different problem in my case. Opened a new issue #24625.

JaredCrean2 on 16 Nov 2017

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