From: LIAO Mingling (Mingling1949_at_hotmail.com)
Date: Fri May 04 2018 - 07:07:13 CDT
Dear all,
I am trying to compile NAMD on the upgraded cluster (x86_64 GNU/Linux) from source code with MPI version.
When I typed the command to build and test the Charm++/Converse library:
env MPICXX=mpicxx ./build charm++ mpi-linux-x86_64 --with-production
I got the following error. Does anyone know how to solve this problem? Thanks in advance!
ERROR:
###########
[1525432978.493880] [login01:30113:0] sys.c:744 MXM WARN Conflicting CPU frequencies detected, using: 2000.00
[1525432978.504097] [login01:30114:0] sys.c:744 MXM WARN Conflicting CPU frequencies detected, using: 2000.00
[1525432978.507528] [login01:30111:0] sys.c:744 MXM WARN Conflicting CPU frequencies detected, using: 2000.00
[1525432978.514122] [login01:30112:0] sys.c:744 MXM WARN Conflicting CPU frequencies detected, using: 2000.00
[login01:30113:0] Caught signal 11 (Segmentation fault)
[login01:30114:0] Caught signal 11 (Segmentation fault)
[login01:30111:0] Caught signal 11 (Segmentation fault)
[login01:30112:0] Caught signal 11 (Segmentation fault)
==== backtrace ====
2 0x00000000000687bc mxm_handle_error() /var/tmp/OFED_topdir/BUILD/mxm-3.6.3104/src/mxm/util/debug/debug.c:641
3 0x0000000000068d0c mxm_error_signal_handler() /var/tmp/OFED_topdir/BUILD/mxm-3.6.3104/src/mxm/util/debug/debug.c:616
4 0x0000000000035270 killpg() ??:0
5 0x000000000002ccb0 ompi_comm_dup_with_info() /var/tmp/OFED_topdir/BUILD/openmpi-3.0.0rc6/ompi/communicator/comm.c:976
6 0x000000000005cba6 PMPI_Comm_dup() /var/tmp/OFED_topdir/BUILD/openmpi-3.0.0rc6/ompi/mpi/c/profile/pcomm_dup.c:63
7 0x00000000006bff0d ConverseInit() ??:0
8 0x0000000000591799 main() ??:0
9 0x0000000000021c05 __libc_start_main() ??:0
10 0x00000000004c66b9 _start() ??:0
===================
==== backtrace ====
2 0x00000000000687bc mxm_handle_error() /var/tmp/OFED_topdir/BUILD/mxm-3.6.3104/src/mxm/util/debug/debug.c:641
3 0x0000000000068d0c mxm_error_signal_handler() /var/tmp/OFED_topdir/BUILD/mxm-3.6.3104/src/mxm/util/debug/debug.c:616
4 0x0000000000035270 killpg() ??:0
5 0x000000000002ccb0 ompi_comm_dup_with_info() /var/tmp/OFED_topdir/BUILD/openmpi-3.0.0rc6/ompi/communicator/comm.c:976
6 0x000000000005cba6 PMPI_Comm_dup() /var/tmp/OFED_topdir/BUILD/openmpi-3.0.0rc6/ompi/mpi/c/profile/pcomm_dup.c:63
7 0x00000000006bff0d ConverseInit() ??:0
8 0x0000000000591799 main() ??:0
9 0x0000000000021c05 __libc_start_main() ??:0
10 0x00000000004c66b9 _start() ??:0
===================
==== backtrace ====
2 0x00000000000687bc mxm_handle_error() /var/tmp/OFED_topdir/BUILD/mxm-3.6.3104/src/mxm/util/debug/debug.c:641
3 0x0000000000068d0c mxm_error_signal_handler() /var/tmp/OFED_topdir/BUILD/mxm-3.6.3104/src/mxm/util/debug/debug.c:616
4 0x0000000000035270 killpg() ??:0
5 0x000000000002ccb0 ompi_comm_dup_with_info() /var/tmp/OFED_topdir/BUILD/openmpi-3.0.0rc6/ompi/communicator/comm.c:976
6 0x000000000005cba6 PMPI_Comm_dup() /var/tmp/OFED_topdir/BUILD/openmpi-3.0.0rc6/ompi/mpi/c/profile/pcomm_dup.c:63
7 0x00000000006bff0d ConverseInit() ??:0
8 0x0000000000591799 main() ??:0
9 0x0000000000021c05 __libc_start_main() ??:0
10 0x00000000004c66b9 _start() ??:0
===================
==== backtrace ====
2 0x00000000000687bc mxm_handle_error() /var/tmp/OFED_topdir/BUILD/mxm-3.6.3104/src/mxm/util/debug/debug.c:641
3 0x0000000000068d0c mxm_error_signal_handler() /var/tmp/OFED_topdir/BUILD/mxm-3.6.3104/src/mxm/util/debug/debug.c:616
4 0x0000000000035270 killpg() ??:0
5 0x000000000002ccb0 ompi_comm_dup_with_info() /var/tmp/OFED_topdir/BUILD/openmpi-3.0.0rc6/ompi/communicator/comm.c:976
6 0x000000000005cba6 PMPI_Comm_dup() /var/tmp/OFED_topdir/BUILD/openmpi-3.0.0rc6/ompi/mpi/c/profile/pcomm_dup.c:63
7 0x00000000006bff0d ConverseInit() ??:0
8 0x0000000000591799 main() ??:0
9 0x0000000000021c05 __libc_start_main() ??:0
10 0x00000000004c66b9 _start() ??:0
===================
#################
COMMANDS:
###################
$ source /etc/profile.d/modules.sh
$ module load impi
$ module load intel
$ tar xzf NAMD_2.12_Source.tar.gz
$ cd NAMD_2.12_Source
$ wget http://www.ks.uiuc.edu/Research/namd/libraries/fftw-linux-x86_64.tar.gz
$ tar xzf fftw-linux-x86_64.tar.gz
$ mv linux-x86_64 fftw
$ wget http://www.ks.uiuc.edu/Research/namd/libraries/tcl8.5.9-linux-x86_64.tar.gz
$ wget http://www.ks.uiuc.edu/Research/namd/libraries/tcl8.5.9-linux-x86_64-threaded.tar.gz
$ tar xzf tcl8.5.9-linux-x86_64.tar.gz
$ tar xzf tcl8.5.9-linux-x86_64-threaded.tar.gz
$ mv tcl8.5.9-linux-x86_64 tcl
$ mv tcl8.5.9-linux-x86_64-threaded tcl-threaded
$ tar xf charm-6.7.1.tar
$ cd charm-6.7.1
$ env MPICXX=mpicxx ./build charm++ mpi-linux-x86_64 --with-production
$ cd mpi-linux-x86_64/tests/charm++/megatest
$ make pgm
$ mpiexec -n 4 ./pgm
############################
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