如何修复符号查找错误:群集环境中的未定义符号错误

Question

我正在研究一些python代码,它使用GDAL(http://www.gdal.org/)及其python绑定从ECW文件中提取一些图像数据.GDAL是从源代码构建的,以获得ECW支持.

该程序在我进入的集群服务器上运行.我已经通过ssh终端测试了程序,运行正常.但是,我现在想使用qsub向集群提交作业,但它报告以下内容:

Traceback (most recent call last):
  File "./gdal-test.py", line 5, in <module>
    from osgeo import gdal
  File "/home/h3/ctargett/.local/lib/python2.6/site-packages/GDAL-1.11.1-py2.6-linux-x86_64.egg/osgeo/__init__.py", line 21, in <module>
    _gdal = swig_import_helper()
  File "/home/h3/ctargett/.local/lib/python2.6/site-packages/GDAL-1.11.1-py2.6-linux-x86_64.egg/osgeo/__init__.py", line 17, in swig_import_helper
    _mod = imp.load_module('_gdal', fp, pathname, description)
ImportError: /mnt/aeropix/prgs/.local/lib/libgdal.so.1: undefined symbol: H5Eset_auto2

我做了一些挖掘,并尝试使用LD_DEBUG=symbols尝试找出差异的地方,但这就是我的知识/理解带给我的.

作为参考,这里是LD_DEBUG=symbols在ssh终端中运行和运行代码的事情(通过管道grep H5Eset_auto2来减少一些输出):

在ssh终端中运行的代码的符号调试输出:

 11359: symbol=H5Eset_auto2;  lookup in file=/usr/bin/python26 [0]
 11359: symbol=H5Eset_auto2;  lookup in file=/usr/lib64/libpython2.6.so.1.0 [0]
 11359: symbol=H5Eset_auto2;  lookup in file=/lib64/libpthread.so.0 [0]
 11359: symbol=H5Eset_auto2;  lookup in file=/lib64/libdl.so.2 [0]
 11359: symbol=H5Eset_auto2;  lookup in file=/lib64/libutil.so.1 [0]
 11359: symbol=H5Eset_auto2;  lookup in file=/lib64/libm.so.6 [0]
 11359: symbol=H5Eset_auto2;  lookup in file=/lib64/libc.so.6 [0]
 11359: symbol=H5Eset_auto2;  lookup in file=/lib64/ld-linux-x86-64.so.2 [0]
 11359: symbol=H5Eset_auto2;  lookup in file=/home/h3/ctargett/.local/lib/python2.6/site-packages/GDAL-1.11.1-py2.6-linux-x86_64.egg/osgeo/_gdal.so [0]
 11359: symbol=H5Eset_auto2;  lookup in file=/usr/lib64/libpython2.6.so.1.0 [0]
 11359: symbol=H5Eset_auto2;  lookup in file=/mnt/aeropix/prgs/.local/lib/libgdal.so.1 [0]
 11359: symbol=H5Eset_auto2;  lookup in file=/usr/lib64/libstdc++.so.6 [0]
 11359: symbol=H5Eset_auto2;  lookup in file=/lib64/libm.so.6 [0]
 11359: symbol=H5Eset_auto2;  lookup in file=/lib64/libgcc_s.so.1 [0]
 11359: symbol=H5Eset_auto2;  lookup in file=/lib64/libpthread.so.0 [0]
 11359: symbol=H5Eset_auto2;  lookup in file=/lib64/libc.so.6 [0]
 11359: symbol=H5Eset_auto2;  lookup in file=/lib64/libdl.so.2 [0]
 11359: symbol=H5Eset_auto2;  lookup in file=/lib64/libutil.so.1 [0]
 11359: symbol=H5Eset_auto2;  lookup in file=/mnt/aeropix/prgs/.local/lib/libhdf5.so.7 [0]
 11359: symbol=H5Eset_auto2;  lookup in file=/usr/bin/python26 [0]
 11359: symbol=H5Eset_auto2;  lookup in file=/usr/lib64/libpython2.6.so.1.0 [0]
 11359: symbol=H5Eset_auto2;  lookup in file=/lib64/libpthread.so.0 [0]
 11359: symbol=H5Eset_auto2;  lookup in file=/lib64/libdl.so.2 [0]
 11359: symbol=H5Eset_auto2;  lookup in file=/lib64/libutil.so.1 [0]
 11359: symbol=H5Eset_auto2;  lookup in file=/lib64/libm.so.6 [0]
 11359: symbol=H5Eset_auto2;  lookup in file=/lib64/libc.so.6 [0]
 11359: symbol=H5Eset_auto2;  lookup in file=/lib64/ld-linux-x86-64.so.2 [0]
 11359: symbol=H5Eset_auto2;  lookup in file=/home/h3/ctargett/.local/lib/python2.6/site-packages/GDAL-1.11.1-py2.6-linux-x86_64.egg/osgeo/_gdal.so [0]
 11359: symbol=H5Eset_auto2;  lookup in file=/usr/lib64/libpython2.6.so.1.0 [0]
 11359: symbol=H5Eset_auto2;  lookup in file=/mnt/aeropix/prgs/.local/lib/libgdal.so.1 [0]
 11359: symbol=H5Eset_auto2;  lookup in file=/usr/lib64/libstdc++.so.6 [0]
 11359: symbol=H5Eset_auto2;  lookup in file=/lib64/libm.so.6 [0]
 11359: symbol=H5Eset_auto2;  lookup in file=/lib64/libgcc_s.so.1 [0]
 11359: symbol=H5Eset_auto2;  lookup in file=/lib64/libpthread.so.0 [0]
 11359: symbol=H5Eset_auto2;  lookup in file=/lib64/libc.so.6 [0]
 11359: symbol=H5Eset_auto2;  lookup in file=/lib64/libdl.so.2 [0]
 11359: symbol=H5Eset_auto2;  lookup in file=/lib64/libutil.so.1 [0]
 11359: symbol=H5Eset_auto2;  lookup in file=/mnt/aeropix/prgs/.local/lib/libhdf5.so.7 [0]

使用qsub提交的代码的符号调试输出:

 16915: symbol=H5Eset_auto2;  lookup in file=/usr/bin/python26 [0]
 16915: symbol=H5Eset_auto2;  lookup in file=/usr/lib64/libpython2.6.so.1.0 [0]
 16915: symbol=H5Eset_auto2;  lookup in file=/lib64/libpthread.so.0 [0]
 16915: symbol=H5Eset_auto2;  lookup in file=/lib64/libdl.so.2 [0]
 16915: symbol=H5Eset_auto2;  lookup in file=/lib64/libutil.so.1 [0]
 16915: symbol=H5Eset_auto2;  lookup in file=/lib64/libm.so.6 [0]
 16915: symbol=H5Eset_auto2;  lookup in file=/lib64/libc.so.6 [0]
 16915: symbol=H5Eset_auto2;  lookup in file=/lib64/ld-linux-x86-64.so.2 [0]
 16915: symbol=H5Eset_auto2;  lookup in file=/home/h3/ctargett/.local/lib/python2.6/site-packages/GDAL-1.11.1-py2.6-linux-x86_64.egg/osgeo/_gdal.so [0]
 16915: symbol=H5Eset_auto2;  lookup in file=/usr/lib64/libpython2.6.so.1.0 [0]
 16915: symbol=H5Eset_auto2;  lookup in file=/mnt/aeropix/prgs/.local/lib/libgdal.so.1 [0]
 16915: symbol=H5Eset_auto2;  lookup in file=/usr/lib64/libstdc++.so.6 [0]
 16915: symbol=H5Eset_auto2;  lookup in file=/lib64/libm.so.6 [0]
 16915: symbol=H5Eset_auto2;  lookup in file=/lib64/libgcc_s.so.1 [0]
 16915: symbol=H5Eset_auto2;  lookup in file=/lib64/libpthread.so.0 [0]
 16915: symbol=H5Eset_auto2;  lookup in file=/lib64/libc.so.6 [0]
 16915: symbol=H5Eset_auto2;  lookup in file=/lib64/libdl.so.2 [0]
 16915: symbol=H5Eset_auto2;  lookup in file=/lib64/libutil.so.1 [0]
 16915: symbol=H5Eset_auto2;  lookup in file=/mnt/aeropix/prgs/.local/lib/libhdf5.so.7 [0]
 16915: symbol=H5Eset_auto2;  lookup in file=/usr/lib64/libjpeg.so.62 [0]
 16915: symbol=H5Eset_auto2;  lookup in file=/usr/lib64/libpng12.so.0 [0]
 16915: symbol=H5Eset_auto2;  lookup in file=/usr/lib64/libpq.so.4 [0]
 16915: symbol=H5Eset_auto2;  lookup in file=/usr/lib64/libcurl.so.3 [0]
 16915: symbol=H5Eset_auto2;  lookup in file=/usr/lib64/libgssapi_krb5.so.2 [0]
 16915: symbol=H5Eset_auto2;  lookup in file=/usr/lib64/libkrb5.so.3 [0]
 16915: symbol=H5Eset_auto2;  lookup in file=/usr/lib64/libk5crypto.so.3 [0]
 16915: symbol=H5Eset_auto2;  lookup in file=/lib64/libcom_err.so.2 [0]
 16915: symbol=H5Eset_auto2;  lookup in file=/usr/lib64/libidn.so.11 [0]
 16915: symbol=H5Eset_auto2;  lookup in file=/lib64/libssl.so.6 [0]
 16915: symbol=H5Eset_auto2;  lookup in file=/lib64/libcrypto.so.6 [0]
 16915: symbol=H5Eset_auto2;  lookup in file=/mnt/aeropix/prgs/.local/lib/libNCSEcw.so.0 [0]
 16915: symbol=H5Eset_auto2;  lookup in file=/mnt/aeropix/prgs/.local/lib/libNCSEcwC.so.0 [0]
 16915: symbol=H5Eset_auto2;  lookup in file=/mnt/aeropix/prgs/.local/lib/libNCSCnet.so.0 [0]
 16915: symbol=H5Eset_auto2;  lookup in file=/mnt/aeropix/prgs/.local/lib/libNCSUtil.so.0 [0]
 16915: symbol=H5Eset_auto2;  lookup in file=/lib64/librt.so.1 [0]
 16915: symbol=H5Eset_auto2;  lookup in file=/usr/lib64/libxml2.so.2 [0]
 16915: symbol=H5Eset_auto2;  lookup in file=/mnt/aeropix/prgs/.local/lib/libz.so.1 [0]
 16915: symbol=H5Eset_auto2;  lookup in file=/lib64/ld-linux-x86-64.so.2 [0]
 16915: symbol=H5Eset_auto2;  lookup in file=/lib64/libcrypt.so.1 [0]
 16915: symbol=H5Eset_auto2;  lookup in file=/lib64/libresolv.so.2 [0]
 16915: symbol=H5Eset_auto2;  lookup in file=/lib64/libnsl.so.1 [0]
 16915: symbol=H5Eset_auto2;  lookup in file=/usr/lib64/libkrb5support.so.0 [0]
 16915: symbol=H5Eset_auto2;  lookup in file=/lib64/libkeyutils.so.1 [0]
 16915: symbol=H5Eset_auto2;  lookup in file=/lib64/libselinux.so.1 [0]
 16915: symbol=H5Eset_auto2;  lookup in file=/lib64/libsepol.so.1 [0]
 16915: /mnt/aeropix/prgs/.local/lib/libgdal.so.1: error: symbol lookup error: undefined symbol: H5Eset_auto2 (fatal)
ImportError: /mnt/aeropix/prgs/.local/lib/libgdal.so.1: undefined symbol: H5Eset_auto2

我想我不知道为什么它似乎停止在使用qsub提交时查看libgdal.so.1,当它继续看起来只是在终端中运行时.我还注意到qsub作业能够正确定位libhdf5.so.7(它应该找到的位置H5Eset_auto2),因为它可以找到不同的符号,H5Eprint:

 16915: symbol=H5Eprint;  lookup in file=/usr/lib64/libpython2.6.so.1.0 [0]
 16915: symbol=H5Eprint;  lookup in file=/mnt/aeropix/prgs/.local/lib/libgdal.so.1 [0]
 16915: symbol=H5Eprint;  lookup in file=/usr/lib64/libstdc++.so.6 [0]
 16915: symbol=H5Eprint;  lookup in file=/lib64/libm.so.6 [0]
 16915: symbol=H5Eprint;  lookup in file=/lib64/libgcc_s.so.1 [0]
 16915: symbol=H5Eprint;  lookup in file=/lib64/libpthread.so.0 [0]
 16915: symbol=H5Eprint;  lookup in file=/lib64/libc.so.6 [0]
 16915: symbol=H5Eprint;  lookup in file=/lib64/libdl.so.2 [0]
 16915: symbol=H5Eprint;  lookup in file=/lib64/libutil.so.1 [0]
 16915: symbol=H5Eprint;  lookup in file=/mnt/aeropix/prgs/.local/lib/libhdf5.so.7 [0]

关于这一点的任何指针在这个阶段都会非常有用(我希望有足够的信息 - 我非常乐意提供更多信息,我只是不确定在这个阶段还有什么用处).

编辑:

/usr/bin对于使用qsub(特别libtool是缺失)提交的作业,似乎内容不同.这正在调查中.

Answer 1

经过两十条评论来了解情况后,发现libhdf5.so.7实际上是一个符号链接(具有多个间接级别)到一个文件,该文件在排队进程和交互式进程之间没有共享.这意味着即使符号链接本身位于共享文件系统上,文件的内容也不会,因此进程看到了库的不同版本.

供将来参考:除了检查之外LD_LIBRARY_PATH,检查库nm -D以查看符号是否确实存在总是一个好主意.在这种情况下,发现它们确实以交互模式存在,但在队列中运行时不存在.很快就md5sum发现文件实际上是不同的.