AMBER Archive (2009)

Subject: [AMBER] amber parallel test fail

From: Nahoum Anthony (nahoum.anthony_at_strath.ac.uk)
Date: Fri Oct 23 2009 - 05:20:45 CDT

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

_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber