AMBER Archive (2009)

Subject: [AMBER] amber parallel test fail

From: Nahoum Anthony (
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




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 with mdout.dinucAU_pln



diffing with dinuc_pln_vs_t



cd bintraj && ./Run.bintraj

diffing with nc_headers



make[1]: Leaving directory `/home/amber/AMBER/amber10/test'

export TESTsander=/home/amber/AMBER/amber10/exe/sander.MPI; cd 4096wat &&

diffing with mdout.column_fft



export TESTsander=/home/amber/AMBER/amber10/exe/sander.MPI; cd jar_multi &&


 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 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,



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