AMBER Archive (2006)

Subject: AMBER: Amber9 under SGI Prism (Altix) with Intel 8.0 error in pbpgb test

From: David McGiven (david.mcgiven_at_fusemail.com)
Date: Wed Jun 21 2006 - 05:46:40 CDT

Dear Amber users,

We recently bought amber 9 and I compiled it in one of our SGI machines.

The Machine is an SGI Prism (Basically an Altix with Graphics) running
SLES9 with SGI ProPack 4SP3 for Linux, Build 403r1-0512182217

I compiled the amber9 source tarball with Intel 8.0 compilers :

Those are the versions I used :

l_cc_pc_8.1.032.tar.gz
l_fc_pc_8.1.028.tar.gz

I ran ./configure -nopar sgi_altix
make serial

The compilation was ok and then I started to run the tests. Everything
was going fine till it reached the pbpgb test. It crashes with the
following error :

==============================================================
cd alp; ./Run.alp
diffing mdout.alp.save with mdout.alp
PASSED
==============================================================
cd pb_pgb; ./Run.pbpgb
getRegFromUnwindContext: Can't get Gr0 from UnwindContext, using 0
forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image PC Routine Line
Source sander 40000000000AC821 Unknown
Unknown Unknown sander 4000000000095300 Unknown
Unknown Unknown sander 400000000008FA30 Unknown
Unknown Unknown sander 40000000005EEBA0 Unknown
Unknown Unknown sander 40000000001CB390 Unknown
Unknown Unknown sander 4000000000177EF0
Unknown Unknown Unknown sander
4000000000176730 Unknown Unknown Unknown sander
4000000000003E90 Unknown Unknown Unknown libc.so.6.1
2000000001AB9C50 Unknown Unknown Unknown sander
4000000000003840 Unknown Unknown Unknown
./Run.pbpgb: Program error make: *** [test.sander.BASIC] Error 1

At the same time, in another folder, I was compiling it with mpi support

I ran ./configure -mpi sgi_altix
make parallel

Again, the compilation was ok and then I started to run the tests.
Everything was going fine till it reached the pbpgb test again!. It
crashes with the following error :

==============================================================
cd alp; ./Run.alp
diffing mdout.alp.save with mdout.alp
PASSED
==============================================================
cd pb_pgb; ./Run.pbpgb
MPI: On host incal, Program /opt/soft/amber9-mpi-mkl/exe/sander.MPI,
Rank 0, Process 16286 received signal SIGSEGV(11)

MPI: --------stack traceback-------
sh: line 1: idb: command not found

MPI: -----stack traceback ends-----
MPI: On host incal, Program /opt/soft/amber9-mpi-mkl/exe/sander.MPI,
Rank 0, Process 16286: Dumping core on signal SIGSEGV(11) into directory
/opt/soft/amber9-mpi-mkl/test/pb_pgb MPI: MPI_COMM_WORLD rank 0 has
terminated without calling MPI_Finalize() MPI: aborting job
MPI: Received signal 11

  ./Run.pbpgb: Program error
make[1]: *** [test.sander.BASIC] Error 1
make[1]: Leaving directory `/opt/soft/amber9-mpi-mkl/test'
make: *** [test.sander.BASIC.MPI] Error 2

Best Regards,
David McGiven
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