Dear AMBER7 users,
I have compiled AMBER7 on an SGI machine with the following CPUs:
300 MHZ IP27 Processors
CPU: MIPS R12000 Processor Chip Revision: 2.3
FPU: MIPS R12010 Floating Point Chip Revision: 2.3
The OS is IRIX 6.5.20m.
The MACHINE file I am using is $AMBERHOME/src/Machines/Machine.sgi_nopar
(unedited from the distribution CD)
I ran the test suite ($AMBERHOME/test/make test.sander)
The error message is rather unhelpful, but here goes:
---snip---
cd dmp; ./Run.dmp
Bus error (core dumped)
Program error
make: *** [test.sander] Error 1
---snip---
and that's as far as it gets.
The mdout file ends like this:
---snip---
--------------------------------------------------------------------------------
3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------
dmp
begin time read from input coords = 0.000 ps
Number of triangulated 3-point waters found: 0
---snip---
Please can anyone shed some light on this problem?
My eventual goal is to compile and run the MPI parallel version using
$AMBERHOME/src/Machines/Machine.sgi_mpi. I have tried to do this
compilation too, and have found a problem with sander too:
---snip---
cd dmp; ./Run.dmp
This test not set up for parallel
cannot run in parallel with #residues < #pes
cd adenine; ./Run.adenine
This test not set up for parallel
cannot run in parallel with #residues < #pes
==============================================================
cd cytosine; ./Run.cytosine
MPI: On host ukwsv100, Program ../../exe/sander, Rank 0, Process 12101637
received signal SIGBUS(10)
MPI: --------stack traceback-------
12101637(7):
0x8765080[MPI_SGI_stacktraceback]
0x87655a8[first_arriver_handler]
0x8765858[slave_sig_handler]
0xa6ba1c8[flush_]
0x1011e47c[amflsh_]
0x1000a850[MAIN__]
0xade9d74[main]
MPI: dbx version 7.2.1 patch 2991 May 14 1998 17:09:10
MPI: Unknown processor type 0xe, assuming R4000.
MPI: Process 12101637 (sander) stopped at [__waitsys:24 +0x8,0xfaaf3f8]
MPI: Source (of
/xlv46/6.5.20m/work/irix/lib/libc/libc_n32_M4/proc/waitsys.s) not available
for Process 12101637
MPI: > 0 __waitsys(0x0, 0xbbc25d, 0x7fff1870, 0x3, 0x0, 0x7fffffd3,
0xfb32cd0, 0x16)
["/xlv46/6.5.20m/work/irix/lib/libc/libc_n32_M4/proc/waitsys.s":24,
0xfaaf3f8]
MPI: 1 _waitpid(0xbbc25d, 0x7fff1a08, 0x7fff1870, 0x3, 0x0, 0x7fffffd3,
0xfb32cd0, 0x16)
["/xlv46/6.5.20m/work/irix/lib/libc/libc_n32_M4/proc/uwaitpid.c":47,
0xfab02b8]
MPI: 2 mpi_sgi_system(0x0, 0xbbc25d, 0x7fff1870, 0x3, 0x0, 0x7fffffd3,
0xfb32cd0, 0x16)
["/xlv4/mpt/1.9/mpi/work/4.4/lib/libmpi/libmpi_n32_M4/adi/sig.c":102,
0x8764b5c]
MPI: 3 MPI_SGI_stacktraceback(0x0, 0xbbc25d, 0x7fff1870, 0x3, 0x0,
0x7fffffd3, 0xfb32cd0, 0x16)
["/xlv4/mpt/1.9/mpi/work/4.4/lib/libmpi/libmpi_n32_M4/adi/sig.c":345,
0x87651ec]
MPI: 4 first_arriver_handler(0xa, 0x0, 0x7fff1870, 0x3, 0x0, 0x7fffffd3,
0xfb32cd0, 0x16)
["/xlv4/mpt/1.9/mpi/work/4.4/lib/libmpi/libmpi_n32_M4/adi/sig.c":564,
0x87655a8]
MPI: 5 slave_sig_handler(0xa, 0xbbc25d, 0x7fff1870, 0x3, 0x0,
0x7fffffd3, 0xfb32cd0, 0x16)
["/xlv4/mpt/1.9/mpi/work/4.4/lib/libmpi/libmpi_n32_M4/adi/sig.c":650,
0x8765858]
MPI: 6 _sigtramp()
["/xlv46/6.5.20m/work/irix/lib/libc/libc_n32_M4/signal/sigtramp.s":71,
0xfac53ec]
MPI: -----stack traceback ends-----
MPI: On host ukwsv100, Program ../../exe/sander, Rank 0, Process 12101637:
Dumping core on signal SIGBUS(10) into directory
/proj/comp_chem/apps/CCMM/ucsf/amber/V7.0_PARALLEL/test/cytosine
MPI: MPI_COMM_WORLD rank 0 has terminated without calling MPI_Finalize()
MPI: aborting job
MPI: Received signal 10
Program error
make: *** [test.sander] Error 1
---snip---
Many thanks for any help anyone can give.
Regards, James Woolven
GSK
Stevenage
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Received on Fri Mar 05 2004 - 12:53:00 PST
