CODEWITHSUNDEEP
centosmpi
user2595474
user2595474

Reputation: 1

Error in loading shared libraries

Hello all i am a student of bioinformatics and working on gromacs , while preparing for a simulation , i am getting this error

[root@compute-0-3 bin]# pdb2gmx -f model-317.pdb -water spce

pdb2gmx: error while loading shared libraries: libmpi.so.0: cannot open shared object file: No such file or directory**

How to solve this problem ??

Upvotes: 0

Views: 6022

Answers (2)

Robert Jørgensgaard Engdahl
Robert Jørgensgaard Engdahl

Reputation: 3364

I have found it useful to use strace -eopen COMMAND to see which files are actually searched for, and what return code open gives for each of them. For instance:

$ strace -eopen echo foo
open("/etc/ld.so.cache", O_RDONLY|O_CLOEXEC) = 3
open("/lib/x86_64-linux-gnu/libc.so.6", O_RDONLY|O_CLOEXEC) = 3
open("/usr/lib/locale/locale-archive", O_RDONLY|O_CLOEXEC) = 3
foo

Use this trick to verify if it is just the path that is set wrong.

Also libmpi.so.0 may not be properly installed. You might have the file libmpi.so.0.1.2.3, and you need to either run ldconfig or manually make a symlink from libmpi.so.0 to libmpi.so.0.1.2.3. See more about why shared libraries might have different numbers appended to them here: http://tldp.org/HOWTO/Program-Library-HOWTO/shared-libraries.html

Upvotes: 0

linux_fanatic
linux_fanatic

Reputation: 5177

You have to set the LD_LIBRARY_PATH you can check more on MPI - error loading shared libraries

Thanks & Regards,
Alok Thaker

Upvotes: 1

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