SDSC Gordon Howto

tranquilinho edited this page Feb 8, 2016 · 7 revisions

If you do not have GCC 4.7.2 available, build it

If it is available in, say, ~/gcc, update .bashrc to reflect it:

export PATH=~/gcc/bin:${PATH}
# scipion/software/lib is important later, in order for some programs to find libraries, like libpython
export LD_LIBRARY_PATH=~/gcc/lib64:~/gcc/lib:${PATH}:~/scipion/software/lib

Once gcc 4.7.2 is available, install OpenMPI 1.8.8 from source.

Update also scipion.conf so scipion installer uses the new gcc and OpenMPI:

CC = ~/gcc/bin/gcc
CXX = ~/gcc/bin/g++
MPI_LIB = mpi
MPI_INCLUDE = ~/gcc/include
MPI_BINDIR = ~/gcc/bin
MPI_LIBDIR = ~/gcc/lib
MPI_CXX = ~gcc/bin/mpiCC
MPI_CC = ~/gcc/bin/mpicc

From here, you can proceed with the standard procedure for installing scipion from source code.

When installation is finished, you can configure scipion's hosts.conf:

#PBS -l walltime=%_(JOB_HOURS)s:00:00
QUEUES = { "normal": [["JOB_HOURS", "48", "Time (hours)", "Select the time expected (in hours) for this job"]] }

(you can check details about the queue system in Gordon User Guide web page)

To use the GUI comfortably, you will need some speed-up solution like TurboVNC. Follow some strategy to statically build TurboVNC (for example, use a CentOS 6.5 virtual machine to build turbovnc 2.0.1 from CentOS source RPMS).

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