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Hints and FAQ for Freke
| Q1:
| Warning: no access to tty (Bad file descriptor). Thus no job control in this shell.
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| This message will typically occur in joboutput from the queueing
system.
This is an old and wellknown "bug" in tcsh/csh, just
telling, that no keyboard is attached to the job.
These messages can be safely ignored!
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| Q2:
| Which compilers are availbale, and how to get more informations.
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| The Intel vers. 8.1 compilers are available. See man ifort
and man icc for detailed informations.
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| Q3:
| How to compile, link and run MPI-programs
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| The MPI implementation on Freke is based on the MPI 1.2 standard
enhanced by some of the MPI-2 features.
To compile and link, use:
ifort myprogram.f -lmpi
To run the MPI-program, use:
mpirun -np 4 ./a.out
The corresponding batchjob must be submitted with: qsub -l ncpus=4
jobscript
See also man mpi and man mpirun
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| Q4:
| Which mathamatical libraries are available
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| MKL, the Intel Math Kernel Library vers. 7.2 and
SCSL, the Scientific Computing Software Library are installed.
To use MKL follow this recipe:
ifort -O3 -static-libcxa -o diag diag.f -L/opt/intel/mkl72/lib/64 \
-lmkl_lapack -lguide -lmkl_ipf
To use the SCSL library, use:
ifort -O3 -o diag diag.f -lscs
See man scsl for further informations about the Cray Library.
See also man sdsm for informations about routines for
distributed shared memory. This encompasses the BLACS, SCALAPACK and PBLAS
libraries.
See Intel's
MKL homepage for further informations about MKL.
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| Q5:
| How to ensure that a job isn't started before another job has terminated
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| When submitting the second job, add these arguments to the qsub
command: -W depend=afterany:jobid. For example:
qsub -W depend=afterany:3405 jobscript.sh
This will ensure that the new job isn't started before the job with jobid
3405 has finished. This can be used to submit a series of (non-urgent or
mutual dependent ) jobs, which are run one after another.
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| Q6:
| How to switch between different versions of the compiler.
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| Currently, the default version of the Intel Fortran compiler is 8.1.024.
(verify this with the command: ifort -V)
To see which versions are available, issue the command: module avail.
Among other things, there are references to ifort90
indicating that the Intel Fortran compiler version 9.0 is installed.
To activate this compiler in the current shell, type module add ifort90.
Type ifort -V again to verify that you've got the right compiler.
If an executable is made with a non-default compiler, remember also to load
the right compiler at runtime, because the shared libraries need to be
the ones corresponding to the right compiler version!
Submit the jobs with the -V flag to qsub
to inherit the compiler environment in batchjobs.
To switch back to the default compiler, do: module rm ifort90
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| Q7:
| How do I review the messages flashing over the screen when I log in.
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| Use this command: nyt
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