Dear Amber users,
I've compiled AMBER in parallel using ifort and the Math Kernel Libraries
after successful installation in serial (passing all tests), make clean and
configure with mpich2 (Myricom's version as we're using Myrinet
interconnect). The make parallel command compiles without problem, but the
jar_multi test fails and aborts the testing process... my terminal has this
output:
...
==============================================================
cd plane_plane_restraint && ./Run.dinuc_pln
SANDER: Dinucleoside restrained with new plane-plane angle
restraint that was defined with new natural
language restraint input.
diffing mdout.dinucAU_pln.save with mdout.dinucAU_pln
PASSED
==============================================================
diffing dinuc_pln_vs_t.save with dinuc_pln_vs_t
PASSED
==============================================================
cd bintraj && ./Run.bintraj
diffing nc_headers.save with nc_headers
PASSED
==============================================================
make[1]: Leaving directory `/home/amber/AMBER/amber10/test'
export TESTsander=/home/amber/AMBER/amber10/exe/sander.MPI; cd 4096wat &&
./Run.column_fft
diffing mdout.column_fft.save with mdout.column_fft
PASSED
==============================================================
export TESTsander=/home/amber/AMBER/amber10/exe/sander.MPI; cd jar_multi &&
./Run.jar
Running multisander version of sander amber10
Total processors = 2
Number of groups = 2
Unit 6 Error on OPEN: mdout.jar.001
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 1
rank 1 in job 197 imp1.sibs.strath.ac.uk_50001 caused collective abort of
all ranks
exit status of rank 1: return code 1
./Run.jar: Program error
make: *** [test.sander.BASIC.MPI] Error 1
For the purpose of this test, I have DO _PARALLEL set to 'mpiexec -n 2' and
I can see sander.MPI appearing on both nodes when I use 'top' to check
processes whilst the test is running... I've checked the Amber archives
mailing list and couldn't find anything to direct me as to what caused that
problem. Anyone got an idea ? anymore information required ?
Best regards and thanks for your time,
Nahoum
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Received on Fri Oct 23 2009 - 03:30:03 PDT
