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++
LINKERFORPROGRAMS =~/gcc/bin/g++
MPI_LINKERFORPROGRAMS = mpiCC
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).

Clone this wiki locally
You can’t perform that action at this time.
You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session.
Press h to open a hovercard with more details.