Using the Cluster
Access
ssh hpcXXXX@130.15.59.64
hpcXXXX@130.15.59.64's password: *****
hpcXXXX@sflogin0$ ssh swlogin1
hpcXXXX@swlogin1's password: *****
The file systems for all of our clusters are shared, so you will be using the same home directory as when you are using the M9000 servers or the standard login node sfnode0. swlogin1 can be used for compilation, program development, and testing only, not for production jobs.
Compiling Code
Intel Compiler Suite
The best compiler to use is the Intel Compiler Suite. This includes compilers for Fortran, C, and C++, as well as MPI and OpenMP support, debuggers and development suite. This software resides in /opt/ics. The versions are:
- Fortran (ifort): Intel(R) Fortran Intel(R) 64 Compiler XE for applications running on Intel(R) 64, Version 12.1 Build 20110811
- C (icc): Intel(R) C Intel(R) 64 Compiler XE for applications running on Intel(R) 64, Version 12.1 Build 20110811
- C++ (icpc): Intel(R) C++ Intel(R) 64 Compiler XE for applications running on Intel(R) 64, Version 12.1 Build 20110811
This compiler suite needs to be activated before use. The command is
use icsmpi
Gnu Compilers
In many cases, especially for public domain software, the preferable compiler is gnu C/C++/Fortran. The system version of these is:
Using built-in specs.
Target: x86_64-redhat-linux
Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info
--with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-bootstrap --enable-shared --enable-threads=posix
--enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions
--enable-gnu-unique-object --enable-languages=c,c++,objc,obj-c++,java,fortran,ada --enable-java-awt=gtk
--disable-dssi --with-java-home=/usr/lib/jvm/java-1.5.0-gcj-1.5.0.0/jre --enable-libgcj-multifile
--enable-java-maintainer-mode --with-ecj-jar=/usr/share/java/eclipse-ecj.jar --disable-libjava-multilib
--with-ppl --with-cloog --with-tune=generic --with-arch_32=i686 --build=x86_64-redhat-linux
Thread model: posix
gcc version 4.4.7 20120313 (Red Hat 4.4.7-11) (GCC)
No special activation is needed to use these, as they reside in a system director. A newer version of this compiler set is available in /opt/gcc-4.8.3 and can be access using the command
use gcc-4.8.3
If MPI is required, it can be loaded through
use openmpi
For applications that cannot be re-compiled (for instance, because the source code is not accessible), a pre-compiled Linux version (x64 for Redhat will do the trick) needs to be obtained.
Running Jobs
As mentioned earlier, program runs for user and application software on the login node are allowed only for test purposes or if interactive use is unavoidable. In the latter case, please get in touch to let us know what you need. Production jobs must be submitted through the Grid Engine load scheduler.
You need to add the following two lines to your script for your job to be scheduled to the Linux SW cluster exclusively:
#$ -q abaqus.q
#$ -l qname=abaqus.q
The abaqus name for the queue that is added here derives from the initial software Abaqus that was (and still is) run on this cluster.
Note that your jobs will run on dedicated threads, i.e. typically up to 12 processes can be scheduled to a single node. The Grid Engine will do the scheduling, i.e. there is no way for the user to determine which processes run on which cores.
Help?
General information about using HPCVL facilities can be found in our FAQ pages. We also supply user support (please send email to help@hpcvl.org or contact us directly), so if you experience problems, we can assist you.
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