我想从存储库安装 openmpi 并需要将其与 GCC 一起使用。问题是我也安装了英特尔库,这会导致如下问题:
mpicc.openmpi --version
mpicc.openmpi: error while loading shared libraries: libimf.so: cannot open shared object file: No such file or directory
我的 GCC 版本是:
gcc (Ubuntu 5.4.0-6ubuntu1~16.04.2) 5.4.0 20160609
我正在尝试使用以下命令安装 openmpi:
sudo aptitude install openmpi-bin libopenmpi-dev
那么,如何才能从存储库安装 OpenMPI,以忽略英特尔库并仅使用 GCC?
编辑
which mpicc.openmpi
/usr/bin/mpicc.openmpi
ldd $(which mpicc.openmpi)
linux-vdso.so.1 => (0x00007fffd6fc0000)
libopen-pal.so.13 => /usr/local/lib/libopen-pal.so.13 (0x00007f9b0c8d0000)
libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007f9b0c6b3000)
libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f9b0c2e9000)
libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f9b0bfe0000)
libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007f9b0bddc000)
librt.so.1 => /lib/x86_64-linux-gnu/librt.so.1 (0x00007f9b0bbd3000)
libutil.so.1 => /lib/x86_64-linux-gnu/libutil.so.1 (0x00007f9b0b9d0000)
libimf.so => not found
libsvml.so => not found
libirng.so => not found
libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00007f9b0b7b9000)
/lib64/ld-linux-x86-64.so.2 (0x000056030ed59000)
libintlc.so.5 => not found
我已经安装了英特尔包英特尔® Parallel Studio XE |英特尔® 软件手动(即,./install_gui.sh)。
编辑2
我尝试使用以下方法重新安装 OpenMPI
sudo apt-get install --reinstall openmpi-bin libopenmpi-dev
与
sudo apt-get purge openmpi-bin libopenmpi-dev
sudo apt-get install openmpi-bin libopenmpi-dev
但它们都没有达到预期的效果,库仍然链接到英特尔库。
英特尔图书馆位于/opt/intel
。
编辑3
ls -l /usr/bin/mpicc.openmpi /usr/bin/opal_wrapper; apt-cache policy openmpi-bin libopenmpi-dev
lrwxrwxrwx 1 root root 12 Feb 25 2016 /usr/bin/mpicc.openmpi -> opal_wrapper
-rwxr-xr-x 1 root root 18928 Feb 25 2016 /usr/bin/opal_wrapper
apt-cache policy openmpi-bin libopenmpi-dev
openmpi-bin:
Installed: 1.10.2-8ubuntu1
Candidate: 1.10.2-8ubuntu1
Version table:
*** 1.10.2-8ubuntu1 500
500 http://at.archive.ubuntu.com/ubuntu xenial/universe amd64 Packages
100 /var/lib/dpkg/status
libopenmpi-dev:
Installed: 1.10.2-8ubuntu1
Candidate: 1.10.2-8ubuntu1
Version table:
*** 1.10.2-8ubuntu1 500
500 http://at.archive.ubuntu.com/ubuntu xenial/universe amd64 Packages
100 /var/lib/dpkg/status
答案1
看起来,英特尔
mpicc.openmpi
从存储库或其链接库之一覆盖了官方版本。这是我从存储库进行官方安装的输出:
~$ dpkg -S /usr/bin/mpicc.openmpi libopenmpi-dev: /usr/bin/mpicc.openmpi ~$ ldd /usr/bin/mpicc.openmpi linux-vdso.so.1 => (0x00007ffd785f4000) libopen-pal.so.13 => /usr/lib/libopen-pal.so.13 (0x00007ff1d848d000) libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007ff1d8270000) libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007ff1d7ea6000) libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007ff1d7ca2000) librt.so.1 => /lib/x86_64-linux-gnu/librt.so.1 (0x00007ff1d7a9a000) libutil.so.1 => /lib/x86_64-linux-gnu/libutil.so.1 (0x00007ff1d7896000) libhwloc.so.5 => /usr/lib/x86_64-linux-gnu/libhwloc.so.5 (0x00007ff1d765c000) /lib64/ld-linux-x86-64.so.2 (0x000056499326f000) libnuma.so.1 => /usr/lib/x86_64-linux-gnu/libnuma.so.1 (0x00007ff1d7450000) libltdl.so.7 => /usr/lib/x86_64-linux-gnu/libltdl.so.7 (0x00007ff1d7246000)
它不依赖那些缺失的库。
要修复此问题,您可以重新安装 libopenmpi:
sudo apt-get install --reinstall openmpi-bin libopenmpi-dev
另请注意
/usr/local/lib/libopen-pal.so.13
。它在/usr/local/lib/
文件夹中,因此其优先级高于官方的优先级/usr/lib/
,兼容性可能会被破坏。使用以下方法检查所有子版本
ls -l /usr/local/lib/libopen-pal.so.13*
然后重命名它们,例如
sudo mv /usr/local/lib/libopen-pal.so.13 /usr/local/lib/libopen-pal.so.13.backup