Re: [AMBER] Error during the test of amber 18 installation

From: Daniel Roe <>
Date: Thu, 3 Oct 2019 13:49:53 -0400


On Wed, Oct 2, 2019 at 10:16 AM Sunita Patel <> wrote:
> CPPTRAJ: Multi frame strip command test.
> File locking failed in ADIOI_Set_lock(fd A,cmd F_SETLKW/7,type
> F_RDLCK/0,whence 0) with return value FFFFFFFF and errno 26.
> - If the file system is NFS, you need to use NFS version 3, ensure that the
> lockd daemon is running on all the machines, and mount the directory with
> the 'noac' option (no attribute caching).
> - If the file system is LUSTRE, ensure that the directory is mounted with
> the 'flock' option.
> ADIOI_Set_lock:: Function not implemented
> ADIOI_Set_lock:offset 0, length 1

This is a system error, not a cpptraj one. Are you using intel mpi? A
brief google search indicates it may be intel mpi related. If so, try
using a different version of intel mpi (or if you don't need parallel
cpptraj, don't worry about it as suggested by Dave).

> /home/external/cbs/sunitap/softwares/amber18/bin/cpptraj: error while
> loading shared libraries: cannot open shared object file: No
> such file or directory

Another system error. Cpptraj was compiled and linked to a shared
libbz2 library that is not present on whatever node you are running
on. Ensure this library is present on the excuting node and/or that
LD_LIBRARY_PATH is properly set.


> ./ Program error
> make[4]: [ntx5] Error 1 (ignored)
> Netcdf MD restart read test, ntx=1
> diffing md1.rst7 with md2.rst7
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Received on Thu Oct 03 2019 - 11:00:03 PDT
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