AMBER Archive (2008)

Subject: AMBER: Segmentation faults trying to run sander mpi

From: Idan Gabdank (gabdank_at_cs.bgu.ac.il)
Date: Wed May 28 2008 - 05:59:09 CDT

Dear AMBERS,
I am trying to run a minimization using sander.mpi and I am receiving
segmentation faults, tried to install newer version of openmpi and
recompile Amber9 but it didn't help.
---------------------------------------------------------------------------------------------
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Error:
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[xeonsrv2:01951] *** Process received signal ***
[xeonsrv2:01951] Signal: Segmentation fault (11)
[xeonsrv2:01951] Signal code: Address not mapped (1)
[xeonsrv2:01951] Failing at address: 0x59f4980088
[xeonsrv2:01951] [ 0] /lib/libc.so.6 [0x2b60d4446130]
[xeonsrv2:01951] [ 1]
/usr/lib64/mpi/mpi-openmpi/usr/lib64/openmpi/mca_btl_sm.so(mca_btl_sm_component_progress+0x533)
[0x2b60d96c5b5c]
[xeonsrv2:01951] [ 2]
/usr/lib64/mpi/mpi-openmpi/usr/lib64/openmpi/mca_bml_r2.so(mca_bml_r2_progress+0x24)
[0x2b60d92b91d9]
[xeonsrv2:01951] [ 3]
/usr/lib64/mpi/mpi-openmpi/usr/lib64/libopen-pal.so.0(opal_progress+0x49)
[0x2b60d347793a]
[xeonsrv2:01951] [ 4]
/usr/lib64/mpi/mpi-openmpi/usr/lib64/openmpi/mca_oob_tcp.so(mca_oob_tcp_msg_wait+0x1a)
[0x2b60d57b1fb8]
[xeonsrv2:01951] [ 5]
/usr/lib64/mpi/mpi-openmpi/usr/lib64/openmpi/mca_oob_tcp.so(mca_oob_tcp_recv+0x371)
[0x2b60d57b5b5b]
[xeonsrv2:01951] [ 6]
/usr/lib64/mpi/mpi-openmpi/usr/lib64/libopen-rte.so.0(mca_oob_recv_packed+0x33)
[0x2b60d323cfc1]
[xeonsrv2:01951] [ 7]
/usr/lib64/mpi/mpi-openmpi/usr/lib64/openmpi/mca_gpr_proxy.so(orte_gpr_proxy_put+0x20a)
[0x2b60d5bc6be6]
[xeonsrv2:01951] [ 8]
/usr/lib64/mpi/mpi-openmpi/usr/lib64/libopen-rte.so.0(orte_smr_base_set_proc_state+0x281)
[0x2b60d32529a1]
[xeonsrv2:01951] [ 9]
/usr/lib64/mpi/mpi-openmpi/usr/lib64/libmpi.so.0(ompi_mpi_init+0x7f2)
[0x2b60d2fb5012]
[xeonsrv2:01951] [10]
/usr/lib64/mpi/mpi-openmpi/usr/lib64/libmpi.so.0(MPI_Init+0x81)[0x2b60d2fd4071]

[xeonsrv2:01951] [11]
/usr/lib64/mpi/mpi-openmpi/usr/lib64/libmpi_f77.so.0(PMPI_INIT+0x25)
[0x2b60d2d71525]
[xeonsrv2:01951] [12] sander.MPI(MAIN__+0x46) [0x49bb06]
[xeonsrv2:01951] [13] sander.MPI(main+0xe) [0x62bea6]
[xeonsrv2:01951] [14]
/lib/libc.so.6(__libc_start_main+0xf4)[0x2b60d4432b74]
[xeonsrv2:01951] [15] sander.MPI [0x41f279]
[xeonsrv2:01951] *** End of error message ***
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Some info about the system I am using:
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xeonsrv1 ~ # uname -a
Linux xeonsrv1 2.6.23-gentoo-r3 #1 SMP Wed Jan 16 15:37:54 IST 2008
x86_64 Intel(R) Xeon(R) CPU 5140 @ 2.33GHz GenuineIntel GNU/Linux

xeonsrv1 ~ # gcc --version
gcc (GCC) 4.1.2 (Gentoo 4.1.2 p1.0.2)
Copyright (C) 2006 Free Software Foundation, Inc.

xeonsrv1 ~ # gfortran --version
GNU Fortran 95 (GCC) 4.1.2 (Gentoo 4.1.2 p1.0.2)
Copyright (C) 2006 Free Software Foundation, Inc.

from amber9/src/config.h

#################################################
CC= gcc
CPLUSPLUS=g++
CFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -O2 -m64
CPPFLAGS= $(AMBERBUILDFLAGS)

#------------------------------------------------------------------------------

# Fortran preprocessing and compiler.
# FPPFLAGS holds the main Fortran options, such as whether MPI is used.
#------------------------------------------------------------------------------

FPPFLAGS= -I/usr/lib64/mpi/mpi-openmpi/usr/include -P -DMPI
-xassembler-with-cpp -Dsecond=ambsecond $(AMBERBUILDFLAGS)
FPP= cpp -traditional $(FPPFLAGS)
FC= gfortran
FFLAGS= -I/usr/lib64/mpi/mpi-openmpi/usr/include -O0
-fno-second-underscore -march=nocona $(LOCALFLAGS) $(AMBERBUILDFLAGS)
FOPTFLAGS= -O3 -fno-second-underscore -march=nocona $(LOCALFLAGS)
$(AMBERBUILDFLAGS)
FREEFORMAT_FLAG= -ffree-form

#------------------------------------------------------------------------------

# Loader:
#------------------------------------------------------------------------------

LOAD= gfortran $(LOCALFLAGS) $(AMBERBUILDFLAGS)
LOADCC= gcc $(LOCALFLAGS) $(AMBERBUILDFLAGS)
LOADLIB= -L/usr/lib64/mpi/mpi-openmpi/usr/lib64 -Wl,--no-as-needed
-lmpi_f90 -lmpi_f77 -lmpi -lopen-rte -lopen-pal -ldl
-Wl,--export-dynamic -lnsl -lutil -lm -ldl
LM= -lm
LOADPTRAJ= gfortran $(LOCALFLAGS) $(AMBERBUILDFLAGS)
XHOME= /usr/X11R6
XLIBS= -L/usr/X11R6/lib64 -L/usr/X11R6/lib
#################################################

Thank you in advance for your help.
Idan

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