From: Morad Alawneh (alawneh_at_chem.byu.edu)
Date: Mon Aug 21 2006 - 12:00:47 CDT
Dear users,
I have installed successfully NAMD2.6b1 onto my system, the installation
instructions are attached with this email, and the program was working
without any problem.
I followed the same way for installing NAMD2.6b2, but after submitting a
job I received the following message in the error log file:
bash: line 1: 31904 Segmentation fault /usr/bin/env MPIRUN_MPD=0
MPIRUN_HOST=m4a-7-11.local MPIRUN_PORT=40732
MPIRUN_PROCESSES='m4a-7-11i:m4a-7-11i:m4a-7-11i:m4a-7-11i:m4a-7-10i:m4a-7-10i:m4a-7-10i:m4a-7-10i:m4a-7-9i:m4a-7-9i:m4a-7-9i:m4a-7-9i:m4a-7-8i:m4a-7-8i:m4a-7-8i:m4a-7-8i:m4a-7-7i:m4a-7-7i:m4a-7-7i:m4a-7-7i:m4a-7-6i:m4a-7-6i:m4a-7-6i:m4a-7-6i:m4a-7-5i:m4a-7-5i:m4a-7-5i:m4a-7-5i:m4a-7-4i:m4a-7-4i:m4a-7-4i:m4a-7-4i:m4a-6-24i:m4a-6-24i:m4a-6-24i:m4a-6-24i:m4a-6-23i:m4a-6-23i:m4a-6-23i:m4a-6-23i:m4a-6-22i:m4a-6-22i:m4a-6-22i:m4a-6-22i:m4a-6-21i:m4a-6-21i:m4a-6-21i:m4a-6-21i:m4a-6-20i:m4a-6-20i:m4a-6-20i:m4a-6-20i:m4a-6-19i:m4a-6-19i:m4a-6-19i:m4a-6-19i:m4a-6-18i:m4a-6-18i:m4a-6-18i:m4a-6-18i:m4a-6-17i:m4a-6-17i:m4a-6-17i:m4a-6-17i:m4a-6-16i:m4a-6-16i:m4a-6-16i:m4a-6-16i:m4a-6-15i:m4a-6-15i:m4a-6-15i:m4a-6-15i:m4a-6-14i:m4a-6-14i:m4a-6-14i:m4a-6-14i:m4a-6-13i:m4a-6-13i:m4a-6-13i:m4a-6-13i:m4a-6-12i:m4a-6-12i:m4a-6-12i:m4a-6-12i:m4a-6-11i:m4a-6-11i:m4a-6-11i:m4a-6-11i:m4a-6-10i:m4a-6-10i:m4a-6-10i:m4a-6-10i:m4a-6-9i:m4a-6-9i:m4a-6-9i:m4a-6-9i:m4a-6-8i:m4a-6-8i:m4a-6-8i:m4a-6-8i:m4a-6-7i:m4a-6-7i:m4a-6-7i:m4a-6-7i:m4a-6-6i:m4a-6-6i:m4a-6-6i:m4a-6-6i:m4a-6-5i:m4a-6-5i:m4a-6-5i:m4a-6-5i:m4a-6-4i:m4a-6-4i:m4a-6-4i:m4a-6-4i:m4a-6-3i:m4a-6-3i:m4a-6-3i:m4a-6-3i:m4a-6-2i:m4a-6-2i:m4a-6-2i:m4a-6-2i:m4a-6-1i:m4a-6-1i:m4a-6-1i:m4a-6-1i:'
MPIRUN_RANK=16 MPIRUN_NPROCS=128 MPIRUN_ID=32469
/ibrix/home/mfm42/opt/namd-IB/Linux-amd64-MPI/namd2 +strategy USE_GRID
equil3_sys.namd
Any suggestions for that kind of error will be appreciated.
My system info:
Dell 1855 Linux cluster consisting that is equipped with four Intel Xeon
EM64T processors (3.6GHz) and 8 GB of memory. The nodes are connected
with Infiniband, a high-speed, low-latency copper interconnect.
-- /*Morad Alawneh*/ *Department of Chemistry and Biochemistry* *C100 BNSN, BYU* *Provo, UT 84602*
fftw-2.1.5 Installation:
-------------------------
./configure --prefix=/ibrix/home/mfm42/opt/fftw --enable-threads --enable-mpi --enable-float --enable-type-prefix --enable-debug --enable-dependency-tracking --enable-static
make
make install
###################################################################################
tcl-8.4.13 Installation:
------------------------
./configure --prefix=/ibrix/home/mfm42/opt/tcl --enable-threads --enable-64bit --disable-shared
make
make install
###################################################################################
charm++ Installation:
---------------------
Edit the file charm/src/arch/mpi-linux-amd64/conv-mach.sh:
1)change mpiCC to mpicxx
2)use /ibrix/topspin/mpi/mpich/bin as the path to mpicc and mpicxx.
./build charm++ mpi-linux-amd64 --libdir=/ibrix/topspin/mpi/mpich/lib64 --incdir=/ibrix/topspin/mpi/mpich/include --no-build-shared -O -verbose -DCMK_OPTIMIZE=1 -language charm++ -balance rand
###################################################################################
namd Installation:
------------------
Edit namd/Make.charm
(set CHARMBASE to the full path to charm-??)
Edit various configuration files:
1) namd/arch/Linux-amd64.fftw (fix path to files, and delete all
-I$(HOME)/fftw/include -L$(HOME)/fftw/lib)
2) namd/arch/Linux-amd64.tcl (fix path to files, and delete all
-I$(HOME)/tcl/include -L$(HOME)/tcl/lib)
add -DUSE_NON_CONST to TCLFLAGS
3) namd/arch/Linux-amd64-MPI.arch use /ibrix/topspin/mpi/mpich/bin as a path to
mpicxx and mpicc instead of g++/gcc,
add "CHARMOPTS = -thread pthreads -memory os"
Set up build directory and compile:
./config tcl fftw Linux-amd64-MPI
cd Linux-amd64-MPI
make
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