Author: ssarajlic3

Two new sets of software have been installed on PACE-managed systems – PGI 12.10 and ANSYS 14.5 service pack 1.

PGI 12.10

The Portland Group, Inc. (a.k.a. PGI) makes software compilers and tools for parallel computing. The Portland Group offers optimizing parallel FORTRAN 2003, C99 and C++ compilers and tools for workstations, servers and clusters running Linux, MacOS or Windows operating systems based on the following microprocessors:

This version of the compiler supports the OpenACC GPU programming directives.
More information can be found at The Portland Group website.
Information about using this compiler with the OpenACC directives can be found at PGI Insider and OpenACC.

Usage Example

$ module load pgi/12.10
$ pgfortran example.f90
$ ./a.out
Hello World


ANSYS 14.5 Service Pack 1

ANSYS develops, markets and supports engineering simulation software used to foresee how product designs will behave and how manufacturing processes will operate in real-world environments.

Usage Example

$ module load ansys/14.5
$ ansys145


The Panasas storage server started responding slowly approximately an hour ago. We are using this server to host all of the software stack, and also for the “scratch” directory in your home folders. 

No jobs have been killed, but you will notice significant degradation in the performance. Starting new jobs/commands will be also slow, although they should run.

We are actively working with the vendor to resolve these issues and will keep you updated via this blog and the “pace-availability” email list.

Thank you for your patience.

PACE Team

PACE has several nodes with NVidia GPUs installed.
There are currently two queues (nvidiagpu and nvidia-gpu) that have GPU nodes assigned to them.
It is confusing to have two queues with the same purpose and slightly different names, so PACE will be collapsing both queues into the “nvidia-gpu” queue.
That means that the nvidiagpu queue will disappear, and the nvidia-gpu queue will have all of the resources contained by both queues.

Please send any questions or concerns to pace-support@oit.gatech.edu

We experienced scheduler-related problems this morning (around 10am), which caused jobs to terminate immediately after they are allocated on compute nodes. The system is back to normal, however we are still investigating what caused the issue.

If you have jobs that are affected by this issue, please resubmit them. If you continue to have problems, please contact us as soon as possible.

We are really sorry for this inconvenience.

 

VASP 5.3.2 – Normal, Gamma, and Non-Collinear versions

Version 5.3.2 of VASP has been installed.
The newly installed versions have been checked against our existing tests; the expected results agree to within some small error.
Please check this new version against your known correct results!

Using it

#First, load the required compiler 

$ module load intel/12.1.4 

#Load all the necessary support modules

$ module load mvapich2/1.6 mkl/10.3 fftw/3.3 

#Load the vasp module 

$ module load vasp/5.3.2 

#Run vasp
$ mpirun vasp
#Run the gamma-only version of vasp
$ mpirun vasp_gamma
#Run the noncollinear version of vasp
$ mpirun vasp_noncollinear

Compilation Notes

• Only the Intel compiler generated MPI-enabled vasp binaries that correctly executed the test suite.
• The “vasp” binary was compiled with these preprocessor flags: -DMPI -DHOST=\"LinuxIFC\" -DIFC -DCACHE_SIZE=12000 -DMINLOOP=1 -DPGF90 -Davoidalloc -DNGZhalf -DMPI_BLOCK=8000
• The “vasp_gamma” binary was compiled with these preprocessor flags: -DMPI -DHOST=\"LinuxIFC\" -DIFC -DCACHE_SIZE=12000 -DMINLOOP=1 -DPGF90 -Davoidalloc -DNGZhalf -DwNGZhalf -DMPI_BLOCK=8000
• The “vasp_noncollinear” binary was compiled with these preprocessor flags: -DMPI -DHOST=\"LinuxIFC\" -DIFC -DCACHE_SIZE=12000 -DMINLOOP=1 -DPGF90 -Davoidalloc -DMPI_BLOCK=8000

All of the software detailed below is available through the “modules” system installed on all PACE-managed Redhat Enterprise 6 computers.
For basic usage instructions on PACE systems see the Using Software Modules page.

NCBI BLAST 2.2.25 – Added multithreading in new GCC 4.6.2 version

The 2.2.25 version of BLAST that was compiled with GCC 4.4.5 has multithreading (i.e. multi-CPU execution) disabled.
A new version of BLAST with multithreading enabled has been compiled with the GCC 4.6.2 compiler.

Using it

#First, load the required compiler 

$ module load gcc/4.6.2 

#Now load BLAST 

$ module load ncbi_blast/2.2.25 

#Setup the environment so that blast can find the database 

$ export BLASTDB=/path/to/db 

#Run a nucleotide-nucleotide search 

$ blastn -query /path/to/query/file -db <db_name> -num_threads <number of CPUS allocated to job> 

COMSOL 4.3a – Student and Research versions

COMSOL Multiphysics version 4.3a contains many new functions and additions to the COMSOL product suite. These Release Notes provide information regarding new functionality in existing products and an overview of new products.
See the COMSOL Release Notes for information on updates to this version of COMSOL.

Using it

#Load the research version of comsol 

$ module load comsol/4.3a-research 

$ comsol ... 

#Use the matlab livelink 

$ module load matlab/r2011b 

$ comsol -mlroot ${MATLAB} 

Mathematica 9.0

Mathematica 9 is a major update to the Mathematica software.

Using it

$ module load mathematica/9.0 

$ mathematica 

VASP 5.2.12

The pre-calculated kernel for the vdW-DF functional has been installed into the same directory as the vasp binary.
This precalculated kernel is contained in the file “vdw_kernel.bindat”

Using it

#First, load the vasp module (and all the prerequisites) 

$ module load intel/12.1.4 mvapich2/1.6 mkl/10.2 fftw/3.3 vasp/5.2.12 

#Copy the kernel to where vasp expects (normally the working directory) 

$ cp ${VDW_KERNEL} . 

# Run vasp 

$ mpirun vasp