Software

Error when downloading SRA data on computing nodes

NCBI blocks any connection from computing nodes because they are behind firewalls. Thus OSC users cannot use SRA tools to download data "on-the-fly" at runtime on computing nodes, e.g. 'fastq-dump -X 5 SRR390728'.  OSC users must download SRA data on login using the command 'prefetch' before any sequence analysis. Please see the section 'Download SRA Data'  in the SRA Toolkit software page for more detail.

Segmentation fault from openmpi/1.10-hpcx and 2.0-hpcx on Owens

We have found that recent MPI jobs using openmpi/1.10-hpcx and openmpi/2.0-hpcx on Owens may complete or hang until the job is killed, but receive segmentation fault. Some applications might be affected (if you run these applications with openmpi mentioned above): orca, openfoam and lammps. OSC users can use other compatible versions, e.g. openmpi/1.10.7-hpcx and openmpi/2.1.6-hpcx. Please check available version from the software page.

Gaussian g16b01 G4 problem

Gaussian-4 (G4) theory calculations in Gaussian 16 Rev. B.01 can produce erratic results.  A workaround is to use Gaussian 16 Rev. A.03 or Rev. C.01, e.g.: 

module load gaussian/g16c01

Gaussian 16 Rev. A.03 has been made the default module on all clusters.  A typical symtom is energy blow up in step 8 resulting in an unusually large, erroneous HF/GFHFB2 energy and consequently an incorrect G4 total energy.

Libraries not compatible with cxx17

Libraries for intel/18.0.3 and intel/17.0.7 are not compatible with cxx17.

Intel compilers need gnu library to support 2017 ISO C++ standard, and cxx17 is the module to load the gnu environment for the intel compilers.

You could have errors when you try to compile with the libraries with the default intel environment.

=== update ===

We fixed the issue on Sep 19, 2018. Please contact OSC Help if you have any questions. 

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