Dear Users,
While performing parallel test after Amber18 installation I came across
following errors. It looks like I am missing few prerequisite packages.
Could you please help me to identify which packages I need to install
before I reinstall Amber18 again.
There are several cpptraj.MPI: errors.
It has been long time I am struggling with the installation of Amber18.
Please help me.
Thanks and regards.
Sunita
---------------------
/home/external/cbs/sunitap/softwares/amber18/bin/teLeap: /lib64/libc.so.6:
version `GLIBC_2.14' not found (required by
/home/external/cbs/sunitap/softwares/amber18/bin/teLeap)
/home/external/cbs/sunitap/softwares/amber18/bin/teLeap: /lib64/libc.so.6:
version `GLIBC_2.14' not found (required by
/home/external/cbs/sunitap/softwares/amber18/bin/teLeap)
getpdb: can't open file gbrna.pdb.lpdb
./Run.prm: Program error
make[3]: *** [prm_test] Error 1
-----------------------------------
Please note that PARALLEL PBSA is not implemented in nab.
============================================================================
make[3]: Target `test' not remade because of errors.
make[3]: Leaving directory
`/home/external/cbs/sunitap/softwares/amber18/AmberTools/test/nab'
make[2]: *** [test.nab] Error 2
---------------------------------------
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
File locking failed in ADIOI_Set_lock(fd 0,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
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 1
/home/external/cbs/sunitap/softwares/amber18/bin/cpptraj.MPI: Program error
diffing res1.tz2.crd.save with res1.tz2.crd
possible FAILURE: check res1.tz2.crd.dif
----------------------------------------------------------
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
File locking failed in ADIOI_Set_lock(fd 0,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
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 1
/home/external/cbs/sunitap/softwares/amber18/bin/cpptraj.MPI: Program error
diffing res1.tz2.crd.save with res1.tz2.crd
possible FAILURE: check res1.tz2.crd.dif
-----------------------------------------------------
CPPTRAJ: Center origin 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.
File locking failed in ADIOI_Set_lock(fd 0,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
ADIOI_Set_lock:: Function not implemented
ADIOI_Set_lock:offset 0, length 1
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 1
/home/external/cbs/sunitap/softwares/amber18/bin/cpptraj.MPI: Program error
diffing origin.centered.crd.save with origin.centered.crd
possible FAILURE: check origin.centered.crd.dif
-------------------------------------------- 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
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 1
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
/home/external/cbs/sunitap/softwares/amber18/bin/cpptraj.MPI: Program error
CPPTRAJ: CHARMM DCD Write, step 2.
Error: 'test.ala3.dcd': No such file or directory
Error: Could not set up input trajectory 'test.ala3.dcd'.
1 errors encountered reading input.
Error: Error(s) occurred during execution.
/home/external/cbs/sunitap/softwares/amber18/bin/cpptraj.MPI: Program error
possible FAILURE: file second.ala3.crd does not exist.
---------------------------------------------
Running mpirun -np 2
/home/external/cbs/sunitap/softwares/amber18/bin/rism3d.snglpnt.MPI
/home/external/cbs/sunitap/softwares/amber18/bin/rism3d.snglpnt.MPI not
found... skipping test
make[2]: Target `test.parallel2' not remade because of errors.
make[2]: Leaving directory
`/home/external/cbs/sunitap/softwares/amber18/AmberTools/test'
--------------------------
/home/external/cbs/sunitap/softwares/amber18/bin/cpptraj: error while
loading shared libraries: libbz2.so.1.0: cannot open shared object file: No
such file or directory
./runmd.sh: Program error
make[4]: [ntx5] Error 1 (ignored)
Netcdf MD restart read test, ntx=1
diffing md1.rst7 with md2.rst7
PASSED
---------------------------
On Mon, Sep 30, 2019 at 5:44 PM David Case <david.case.rutgers.edu> wrote:
> On Mon, Sep 30, 2019, Sunita Patel wrote:
> >
> >The test result of parallel installation is as follows.
> >898 file comparisons passed
> >192 file comparisons failed (0 ignored)
> >42 tests experienced errors
> >
> >Is this number of errors during test acceptable to carryout simulation?
>
> No: something is very badly wrong. Look at the log files to see what is
> going on. You will probably see the same error repeated many times, and
> that may get you started in the right direction. You might also ask for
> help from your HPC staff.
>
> ....dac
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Mon Sep 30 2019 - 22:30:02 PDT
