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UME Cluster Specification (Updated on July 24, 2006)
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* General Information
UME Cluster is 21 nodes dual Pentium-III 1.4GHz CPUs and has a global
IP address.
Frontend node: ume.hpcc.jp (163.220.30.64)
Compute node: ume0[0-f].hpcc.jp
ume1[0-3].hpcc.jp
(concated the prefix 'ume' and a serial 2-digit hex number)
Host Certificate: C=JP,O=AIST,OU=GRID,CN=host/ume.hpcc.jp
Host Certificate Issuer: C=JP,O=AIST,OU=GRID,CN=Certificate Authority
url = https://www.apgrid.org/CA/AIST/Production/
crl_url = https://www.apgrid.org/CA/AIST/Production/a317c467.r0
(Note)
Job submission for the PRAGMA routine-basis experiment is limited to the
specific nodes (ume[00-10]) but those nodes are dedicated to the experiment.
* Primitive Software
OS: Linux RedHat 7.3
GNU GCC: /usr/local/GCC/redhat73/2.95.3
/usr/local/GCC/redhat73/3.2.2
/usr/local/GCC/redhat73/3.3
If you set APG_GCCVER variable, your specified gcc will be enabled.
e.g. $ export APG_GCCVER=3.3
$ gcc -v
Intel C++ and Fortran compilers (Ver.7.0): /usr/local/intel
* Grid and Cluster Software
Globus Toolkit (Ver.4.0.1): /usr/local/gt4 (compiled with gcc 2.95.3)
The Jobmanager of PreWS GRAM is "jobmanager-sge".
(you can use globus-job-run and globusrun as is)
The Jobmanager of WS GRAM is SGE.
(you can use globusrun-ws -factory-type SGE)
Grid Engine, version 6.0: /usr/local/sge_root_6.0u1
Ninf-G4 (Ver. 4.1.0): /usr/local/ngv4 (compiled with "flavor=gcc32dbgpthr")
Ninf-G2 (Ver. 2.3.0): /usr/local/ngv2 (compiled with "flavor=gcc32dbgpthr")
Gfarm (Ver. 1.2-6): /usr (installed from RPM)
GridMPI (Ver. 0.11): /usr/local/gridmpi (compiled with gcc 3.3)
MPICH-P4 (Ver. 1.2.5-1a): /usr/local/mpich/ch_p4/bin
MPICH-G2 (Ver. 1.2.5.2):
/usr/local/MPICH/mpich-1.2.5.2/g2-gcc-2.95.3 (compiled with gcc 2.95.3)
/usr/local/MPICH/mpich-1.2.5.2/g2-intel-7.0 (compiled with intel 7.0)
* For Bio-Grid experiment
ncbi est_human database (raw db): /work/pragma/est_human
ncbi toolbox library (compiled with gcc 3.3): /usr/local/ncbi
(Note)
Please set the following variables in the initialization file for your shell.
NCBI_LOCATION=/usr/local/ncbi
LD_LIBRARY_PATH=$NCBI_LOCATION/lib
PATH=$NCBI_LOCATION/bin:$PATH
* For Savannah/Nimrod Experiment
/work/cme is 195 GB diskspace for runtime checkpoint storage.
* For GAMESS-APBS experiment
APBS 0.3.2 Binaries: /usr/local/bin/apbs
examples: /usr/local/apbs-0.3.2/examples
doc: /usr/share/doc/apbs-0.3.2
MALOC (Minimal Abstraction Layer for Object-oriented C)
include: /usr/local/maloc
lib: /usr/local/lib
doc: /usr/share/doc/maloc-0.1
GAMESS June 2005 Binaries: /opt/gamess
(Note)
Please set the following variable in the initialization file for your shell.
LD_LIBRARY_PATH=/usr/local/GCC/redhat73/3.2.2/lib
or LD_LIBRARY_PATH=/usr/local/GCC/redhat73/3.3/lib