undefined symbol: BZ2_bzDecompress

Asked by Carl B. Kissell

Yade is sucessfully installed in the red hat enterprise linux 6 cluster system
while initating, the following error is occured
----------------------------------------------
Welcome to Yade 0.90.3
Traceback (most recent call last):
  File "./yade-0.90.3", line 85, in <module>
    import yade
  File "/home2/Carl/build_5/YADE/lib/yade-0.90.3/py/yade/__init__.py", line 65, in <module>
    import boot
ImportError: /home2/Carl/build_5/YADE/lib/yade-0.90.3/libcore.so: undefined symbol: BZ2_bzDecompress
-----------------------------------------------
Same bug is appeared with Yade 0.97.0 build.
FYI, bzip2 -V
bzip2, a block-sorting file compressor. Version 1.0.5, 10-Dec-2007.

Best
Carl

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Bruno Chareyre (bruno-chareyre) said :
#1

Do you have libbz2 installed? "bzip2 -V" depends on another package it
seems.
This is from debian repos:
libbz2-1.0 -
high-quality block-sorting file compressor library - runtime
bzip2 -
high-quality block-sorting file compressor - utilities

Bruno

Revision history for this message
Carl B. Kissell (tempmapmail) said :
#2

Yes, It is installed and available at /usr/lib64/libbz2.so and linked as below
ldd /usr/lib64/libbz2.so
 linux-vdso.so.1 => (0x00007fff959ff000)
 libc.so.6 => /lib64/libc.so.6 (0x000000309ca00000)
 /lib64/ld-linux-x86-64.so.2 (0x000000309c200000)

Karl

Revision history for this message
Bruno Chareyre (bruno-chareyre) said :
#3

Is libbz2.so a dependency of yade's libcore.so on your system?

ldd lib/libcore.so
  ...
  libbz2.so.1.0 => /lib/x86_64-linux-gnu/libbz2.so.1.0 (0x00007f2ce1703000)

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Anton Gladky (gladky-anton) said :
#4

We do actually use BZip2, but on Debian systems it is, probably
linked to some other libraries, which we use. So we do not need
to do it explicitly. It seems, on RedHat-systems, it is not always so.

I have committed the fix [1]. Please, check it out and let us know,
whether it works for you.

[1] https://github.com/yade/trunk/commit/8ef3fafb1693e881e3404920661b6218389a0647

Cheers,

Anton

2013/10/8 Bruno Chareyre <email address hidden>:
> Question #237009 on Yade changed:
> https://answers.launchpad.net/yade/+question/237009
>
> Status: Open => Answered
>
> Bruno Chareyre proposed the following answer:
> Is libbz2.so a dependency of yade's libcore.so on your system?
> More help : https://help.launchpad.net/ListHelp

Revision history for this message
Carl B. Kissell (tempmapmail) said :
#5

Nope, I dont think so. Please take at look at it from build
ldd /home2/kmohan/build_5/YADE/lib/yade-0.90.3/libcore.so
 linux-vdso.so.1 => (0x00007fff341ff000)
 libsupport.so => /home2/karl/build_5/YADE/lib/yade-0.90.3/libsupport.so (0x00002b62dc315000)
 libpython2.6.so.1.0 => /usr/lib64/libpython2.6.so.1.0 (0x00002b62dc5c9000)
 librt.so.1 => /lib64/librt.so.1 (0x00002b62dc9aa000)
 libstdc++.so.6 => /usr/lib64/libstdc++.so.6 (0x00002b62dcbb2000)
 libm.so.6 => /lib64/libm.so.6 (0x00002b62dceb9000)
 libgomp.so.1 => /usr/lib64/libgomp.so.1 (0x00002b62dd13d000)
 libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00002b62dd34a000)
 libpthread.so.0 => /lib64/libpthread.so.0 (0x00002b62dd561000)
 libc.so.6 => /lib64/libc.so.6 (0x00002b62dd77d000)
 libdl.so.2 => /lib64/libdl.so.2 (0x00002b62ddb1e000)
 libutil.so.1 => /lib64/libutil.so.1 (0x00002b62ddd23000)
 /lib64/ld-linux-x86-64.so.2 (0x000000309c200000)

Karl

Revision history for this message
Carl B. Kissell (tempmapmail) said :
#6

I have compiled your latest github commit and now the following error has appeared,

Welcome to Yade Unknown
Traceback (most recent call last):
  File "./yade-Unknown", line 121, in <module>
    import yade
  File "/home2/Carl/build_6/YADE/lib64/yade-Unknown/py/yade/__init__.py", line 65, in <module>
    import boot
ImportError: /home2/Carl/build_6/YADE/lib64/yade-Unknown/libyade.so: undefined symbol: deflateReset

Carl

Revision history for this message
Anton Gladky (gladky-anton) said :
#7

Very strange, is it an old Redhat-system?

Please, update your code and test again.

https://github.com/yade/trunk/commit/2b0ed69878e46b8f1972058285389c74424e6ecf

Anton

2013/10/9 Carl B. Kissell <email address hidden>:
> Question #237009 on Yade changed:
> https://answers.launchpad.net/yade/+question/237009
>
> Carl B. Kissell gave more information on the question:
> I have compiled your latest github commit and now the following error
> has appeared,
>
> Welcome to Yade Unknown
> Traceback (most recent call last):
> File "./yade-Unknown", line 121, in <module>
> import yade
> File "/home2/Carl/build_6/YADE/lib64/yade-Unknown/py/yade/__init__.py", line 65, in <module>
> import boot
> ImportError: /home2/Carl/build_6/YADE/lib64/yade-Unknown/libyade.so: undefined symbol: deflateReset
>
> Carl
>
> --
> You received this question notification because you are a member of
> yade-users, which is an answer contact for Yade.
>
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> Mailing list: https://launchpad.net/~yade-users
> Post to : <email address hidden>
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> More help : https://help.launchpad.net/ListHelp

Revision history for this message
Carl B. Kissell (tempmapmail) said :
#8

Thanks Anton Gladky, that solved my question.

Revision history for this message
Carl B. Kissell (tempmapmail) said :
#9

I am trying to build yade-0.90.3 in the same system and faced the same bug before. Any suggestions for older version? Thanks for your previous commits.

Revision history for this message
Anton Gladky (gladky-anton) said :
#10

2013/10/10 Carl B. Kissell <email address hidden>:
> I am trying to build yade-0.90.3 in the same system and faced the same
> bug before. Any suggestions for older version?

We do not have resources to support older versions. If you do really need that,
you can backport the following commits [1] and [2]:

[1] https://github.com/yade/trunk/commit/2b0ed69878e46b8f1972058285389c74424e6ecf
[2] https://github.com/yade/trunk/commit/8ef3fafb1693e881e3404920661b6218389a0647

Best regards,

Anton

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