AMBER Archive (2008)

Subject: AMBER: scyld beowulf --amber10--openmpi

From: Rima Chaudhuri (rima.chaudhuri_at_gmail.com)
Date: Mon Oct 20 2008 - 19:00:27 CDT

hello!

I have compiled amber10 parallel in the scyld beowulf cluster using openmpi.
The system is a Intel Xeon, x84_64, and I followed the instructions at
http://archive.ambermd.org/200806/0000.html.
I could successfully compile both sander and pmemd in parallel (or so it said).

However, when I try to test the suite:
cd $AMBERHOME/test
make test.parallel

I get the following error:

bash-2.05b# make test.parallel
export TESTsander=/home/rchaud/Amber10_openmpi/amber10/exe/sander.MPI;
make test.sander.BASIC
make[1]: Entering directory `/home/rchaud/Amber10_openmpi/amber10/test'
cd cytosine && ./Run.cytosine
[helios.structure.uic.edu:17718] [0,0,0] ORTE_ERROR_LOG: Not available
in file ras_bjs.c at line 247
--------------------------------------------------------------------------
Failed to find the following executable:

Host: helios.structure.uic.edu
Executable: -o

Cannot continue.
--------------------------------------------------------------------------
[helios.structure.uic.edu:17718] [0,0,0] ORTE_ERROR_LOG: Not found in
file rmgr_urm.c at line 462
[helios.structure.uic.edu:17718] mpirun: spawn failed with errno=-13
  ./Run.cytosine: Program error
make[1]: *** [test.sander.BASIC] Error 1
make[1]: Leaving directory `/home/rchaud/Amber10_openmpi/amber10/test'
make: *** [test.sander.BASIC.MPI] Error 2

On :
bash-2.05b# mpif90 -show
ifort -I/home/rchaud/openmpi-1.2.6/openmpi-1.2.6_ifort/include
-pthread -I/home/rchaud/openmpi-1.2.6/openmpi-1.2.6_ifort/lib
-L/home/rchaud/openmpi-1.2.6/openmpi-1.2.6_ifort/lib -lmpi_f90
-lmpi_f77 -lmpi -lopen-rte -lopen-pal -ldl -Wl,--export-dynamic -lnsl
-lutil -lm -ldl

If I understand correctly, it cannot find the shared lib files? but I
have defined the LD_LIBRARY_PATH in both the .bashrc and
.bash_profile.
I edited the config_amber.h to add
-L/home/rchaud/openmpi-1.2.6/openmpi-1.2.6_ifort/lib -lmpi_f90
-lmpi_f77 -lmpi -lopen-rte -lopen-pal -ldl -Wl,--export-dynamic -lnsl
-lutil -lm -ldl to LOADLIB, and then did 'make parallel' in
$AMBERHOME/src

which mpirun
/home/rchaud/openmpi-1.2.6/openmpi-1.2.6_ifort/bin/mpirun
However if I echo $LD_LIBRARY_PATH ..it gives me nothing (when logged
in as root), as a regular user, it echos the path
fine.(/home/rchaud/openmpi-1.2.6/openmpi-1.2.6_ifort/lib)

Any cues on what I might be doing wrong?
Also, please find the config_amber.h file attached.

Thanks, 

-- 
-Rima
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