Pharmcluster3 HW/SW Specification
Head Node consists of “2 of Intel(R) Xeon(R) Silver 4310T CPU @ 2.30GHz with total 20 cores”, 128G RAM, 407TB Storage.
Partition “defq”, from node001 to node004: each node consists of “AMD EPYC 7763 64-Core Processor”, 503G RAM, 4 of A4500 GPU(20G)
Partition “extq” from node005 to node008: each node consists of “2 of Intel(R) Xeon(R) CPU E5-2670 0 @ 2.60GHz with total 8 cores”, 64G RAM, 4 of GTX980 (4G)
Partition “rtx” from node011 to node012: each node consists of “2 of Intel(R) Xeon(R) Silver 4210 CPU @ 2.20GHz with total 20 cores”, 93G RAM, 10f RTX2080Ti (12G)
Base OS is Rocky 9 with openHPC 3, and Warewulf3
Jupyter Lab: https://pharmcluster3-ondemand.westernu.edu/pun/sys/dashboard
Scheduler is Slurm, and SW list is:
------------------------------------- /shared/modulefiles --------------------------------------
ADFR/1.0 gtx980/gromacs/2024-mpi (D)
amber/24 gtx980/openmpi/5.0.5
anaconda3/2024.02 lammps/2023-08-02-stable
autodock_vina/1.1.2 mgltools/1.5.7
colabfold/2024 namd/2.14-CPU
gromacs-plumed/2023-2.9.1-mpi namd/2.14-GPU
gromacs-plumed/2023-2.9.1-smp (D) namd/3.0b7-CPU
gromacs/2024.2-mpi namd/3.0b7-GPU (D)
gromacs/2024.2-smp (D) plumed/2.9.1
gtx980/gromacs/2023-2.9.1-mpi-gpu vmd/1.9.3
gtx980/gromacs/2024-mpi-gpu
---------------------------- /opt/ohpc/pub/moduledeps/gnu12-openmpi4 ----------------------------
adios2/2.8.3 mfem/4.4 petsc/3.18.1 scalasca/2.5
boost/1.81.0 mumps/5.2.1 phdf5/1.14.0 scorep/7.1
dimemas/5.4.2 netcdf-cxx/4.3.1 pnetcdf/1.12.3 sionlib/1.7.7
extrae/3.8.3 netcdf-fortran/4.6.0 ptscotch/7.0.1 slepc/3.18.0
fftw/3.3.10 netcdf/4.9.0 py3-mpi4py/3.1.4 superlu_dist/6.4.0
hypre/2.18.1 omb/6.1 py3-scipy/1.5.4 tau/2.31.1
imb/2021.3 opencoarrays/2.10.0 scalapack/2.2.0 trilinos/13.4.0
-------------------------------- /opt/ohpc/pub/moduledeps/gnu12 ---------------------------------
R/4.2.1 likwid/5.2.2 mvapich2/2.3.7 pdtoolkit/3.25.1 scotch/6.0.6
gsl/2.7.1 metis/5.1.0 openblas/0.3.21 plasma/21.8.29 superlu/5.2.1
hdf5/1.14.0 mpich/3.4.3-ofi openmpi4/4.1.5 (L) py3-numpy/1.19.5
----------------------------------- /opt/ohpc/pub/modulefiles -----------------------------------
EasyBuild/4.9.4 cuda/12.3.2 ohpc (L) prun/2.2 (L)
autotools (L) gnu12/12.2.0 (L) os spack/0.22.2
charliecloud/0.15 hwloc/2.11.1 (L) papi/6.0.0 ucx/1.17.0 (L)
cmake/3.24.2 libfabric/1.18.0 (L) pmix/4.2.9 valgrind/3.23.0