isbyeon.tistory.com=>hpccloud.tistory.com

installing BLAS

# tar zxvfp blas.tgz 

# cd BLAS

# make all

installing Lapack

# tar zxvfp lapack-3.4.0.tgz 

# cd lapack-3.4.0

# cp make.inc.example make.inc

# cmake ../lapack-3.4.0

# make

# make install

installing fftw 3.3

# tar zxvfp fftw-3.3.tar.gz

# cd fftw-3.3

# ./configure

# make

# make install

installing fftw 2.1.5

# wget http://www.fftw.org/fftw-2.1.5.tar.gz

# tar zxvfp fftw-2.1.5.tar.gz

# cd fftw-2.1.5

# ./configure

# make

# make install

installing ATLAS

# tar xvfp atlas3.8.3.tar 

# cd ATLAS/

# mkdir linux_x86_64

# cd linux_x86_64

# ../configure -b 64 -D c -DPentiumCPS=2216 -Fa alg -fPIC --with-netlib-lapack=$HOME/src/lapack-3.2.1/lapack_LINUX.a -Si cputhrchk 0 && make && make install

installing CPMD

#./mkconfig.sh LINUX-x86_64-FEDORA-MPI > Makefile

# vi Makefile

===================================================

LFLAGS = -L/usr/local/lib/ -llapack -lblas -lfftw

===================================================

# make

아래와 같은 에러 발생 시
====================================================================================================================
libibverbs: Warning: RLIMIT_MEMLOCK is 32768 bytes.
    This will severely limit memory registrations.
libibverbs: Warning: RLIMIT_MEMLOCK is 32768 bytes.
    This will severely limit memory registrations.
libibverbs: Warning: RLIMIT_MEMLOCK is 32768 bytes.
    This will severely limit memory registrations.
--------------------------------------------------------------------------
The OpenFabrics (openib) BTL failed to initialize while trying to
allocate some locked memory.  This typically can indicate that the
memlock limits are set too low.  For most HPC installations, the
memlock limits should be set to "unlimited".  The failure occured
here:

  Local host:    compute-0-10.local
  OMPI source:   btl_openib_component.c:1066
  Function:      ompi_free_list_init_ex_new()
  Device:        mlx4_0
  Memlock limit: 32768

You may need to consult with your system administrator to get this
problem fixed.  This FAQ entry on the Open MPI web site may also be
helpful:

    http://www.open-mpi.org/faq/?category=openfabrics#ib-locked-pages
--------------------------------------------------------------------------
--------------------------------------------------------------------------
WARNING: There was an error initializing an OpenFabrics device.

  Local host:   compute-0-10.local
  Local device: mlx4_0
--------------------------------------------------------------------------
libibverbs: Warning: RLIMIT_MEMLOCK is 32768 bytes.
    This will severely limit memory registrations.
libibverbs: Warning: RLIMIT_MEMLOCK is 32768 bytes.
    This will severely limit memory registrations.
libibverbs: Warning: RLIMIT_MEMLOCK is 32768 bytes.
    This will severely limit memory registrations.
libibverbs: Warning: RLIMIT_MEMLOCK is 32768 bytes.
    This will severely limit memory registrations.
libibverbs: Warning: RLIMIT_MEMLOCK is 32768 bytes.
    This will severely limit memory registrations.
[compute-0-10.local:02981] 7 more processes have sent help message help-mpi-btl-openib.txt / init-fail-no-mem
[compute-0-10.local:02981] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages
[compute-0-10.local:02981] 7 more processes have sent help message help-mpi-btl-openib.txt / error in device init
====================================================================================================================

1. limits.conf
# vi /etc/security/limits.conf
* soft memlock unlimited
* hard memlock unlimited

2. For using mpirun in SGE session
# qconf -mconf
======================================================
execd_params                 H_MEMORYLOCKED=infinity
======================================================
root@ngscluster1.local modified "global" in configuration list

1. Adding an execution host
Make the new host an administrative host

# qconf -ah <hostname>

As root on this new host, run the following script from $SGE_ROOT

# install_execd

2. Removing an execution host
# qconf -shgrp @allhosts
============================================================================
group_name @allhosts
hostlist test compute-0-0 compute-0-1 compute-0-3 compute-0-4 compute-0-5 \
         compute-0-13f96093_13440deac47__8000
============================================================================

# qconf -shgrp @allhosts > test.txt

# qconf -Mhgrp test.txt
root@sge.kobic.re.kr modified "@allhosts" in host group list

# qconf -shgrp @allhosts
============================================================================
group_name @allhosts
hostlist test compute-0-0 compute-0-1 compute-0-3 compute-0-4 \
         compute-0-13f96093_13440deac47__8000
============================================================================

### Delete the host
# qconf -de compute-0-5

# qconf -dh compute-0-5

### Finally, delete the configuration for the host
# qconf -dconf compute-0-5

#!/usr/bin/perl

$mount = `df -k`;

if($mount !~ /10.1.1.1:\/BiO/)    {

system("mkdir /BiO;mount -t nfs 10.1.1.1:/BiO /BiO";chmod 777 /BiO);
}

# yum install icu libicu.x86_64 libicu-devel.x86_64 libicu-doc.x86_64

# wget http://sourceforge.net/projects/boost/files/boost/1.45.0/boost_1_45_0.tar.bz2/download
# tar xvfjp boost_1_45_0.tar.bz2
# cd boost_1_45_0
# ./bootstrap.sh --with-libraries=program_options,math,graph,test --prefix=/share/apps/boost
# ./bjam install
# cd /usr/lib
# ln -sf /share/apps/boost_1_45_0/lib/libboost_program_options.a libboost_program_options-mt.a
# ln -sf /share/apps/boost_1_45_0/lib/libboost_program_options.so.1.45.0 libboost_program_options-mt.so
# ln -sf /share/apps/boost_1_45_0/lib/libboost_unit_test_framework.a boost_unit_test_framework-mt.a
# ln -sf /share/apps/boost_1_45_0/lib/libboost_unit_test_framework.so libboost_unit_test_framework-mt.so
# ln -sf /share/apps/boost-1.47.0/include/boost/ /usr/include/boost

$ wget http://cs.ru.nl/~jorism/libDAI/libDAI-0.2.7.tar.gz
$ cd libDAI-0.2.7
$ cp Makefile.LINUX Makefile.conf
$ make
$ examples/example tests/alarm.fg
Estimate of needed memory: 48.6562kB
Maximum memory: unlimited
Estimate of needed memory: 48.6562kB
Maximum memory: unlimited