AMBER Archive (2006)

Subject: AMBER: Amber: Parallel Installation Problems

From: Maniopoulou, A \(Mina\) (A.Maniopoulou_at_rl.ac.uk)
Date: Fri Oct 27 2006 - 12:13:56 CDT

Hallo again,

I have compiled the parallel part of Amber using the mpich library (compiled by intel compilers version 8.1), while Amber9 has been compiled with ifort (version 9) and gcc.
I run the tests (using lsf, but interactively ) using 4 processors (apart from the test.sander.EVB that needs 2).
All run successfully apart from test.sander.BASIC.MPI and test.sander.GB.MPI
A1)Test.sander.BASIC.MPI runs till the end, but when Run.noesy is executed I get segmentation fault.

cd noesy; ./Run.noesy
mpirun.lsf -np 4
forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image PC Routine Line Source
sander.MPI 08134CC2 Unknown Unknown Unknown
sander.MPI 08115992 Unknown Unknown Unknown
.............. ................... ..................
TID HOST_NAME COMMAND_LINE STATUS TERMINATION_TIME
==== ========== ================ ======================= ===================
0001 grid-data1 gmmpirun_wrapper Exit (174) 10/27/2006 17:48:21
0002 grid-data1 gmmpirun_wrapper Exit (174) 10/27/2006 17:48:21
0003 grid-data1 gmmpirun_wrapper Exit (174) 10/27/2006 17:48:21
0004 grid-data1 gmmpirun_wrapper Exit (174) 10/27/2006 17:48:21

When I run the Run.noesy script on its own, no segmentation fault appears. I get a possible failure though. And what happens is that noesy.out is identical with noesy.out.save and not noesy.out.mpi.save.

A2) Test.sander.BASIC.MPI errors also, when Run.bintraj is executed.
sander and ptraj: test sander netCDF output and ptraj netCDF input
[0] MPI Abort by user Aborting program !
[0] Aborting program!
Killed by signal 15.
Killed by signal 15.
Killed by signal 15.

TID HOST_NAME COMMAND_LINE STATUS TERMINATION_TIME
==== ========== ================ ======================= ===================
0001 grid-data1 gmmpirun_wrapper Signaled (SIGKILL) 10/27/2006 17:48:50
0002 grid-data1 gmmpirun_wrapper Signaled (SIGKILL) 10/27/2006 17:48:50
0003 grid-data1 gmmpirun_wrapper Signaled (SIGKILL) 10/27/2006 17:48:46
0004 grid-data1 gmmpirun_wrapper Exit (255) 10/27/2006 17:48:43

Terminated
  ./Run.bintraj: Program error
make[1]: [test.sander.BASIC] Error 1 (ignored)

When I run ./Run.bintraj on its own, it runs perfectly.

A3) Test.sander.GB.MPI stops running as soon as Run.gbrna.ips is executed. Again the script runs perfectly on its own.

B1) Then I tried to run some benchmarks and it seems I do not have the following directories under the benchmark dir
  mg_qmmm , ladh, 1NLN_qmmm

B2)Also I do not have the psander executable.

C) Finally, I do not manage to compile pmemd as this message appears during the compilation:
 ifort -c -auto -tpp7 -xN -ip -O3 loadbal.f90
fortcom: Severe: **Internal compiler error: segmentation violation signal raised** Please report this error along with the circumstances in which it occurred in a Software Problem Report. Note: File and line given may not be explicit cause of this error.
The config.h was created by ./configure linux_p4 ifort mpich_gm

Thanks a lot,

Mina Maniopoulou
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