Archived News
2023
2022
2021
2021-10-12
Augustus 3.4.0 has been installed as a
Singularity container.
2021-10-08
FFTW 3.3.10 has been installed. It fixes a
longstanding bug in FFTW3.
GROMACS 2021.3 has been installed.
2021-10-05
Rclone installed. Allows data copy and
sync between Picotte and various cloud storage providers.
2021-09-29
Change in Slurm queueing algorithm: Memory allocation for all
jobs are tracked. Nodes that do not have enough available memory
to meet the jobs memory requirement will not be allocated to the
job.
Troubleshooting guide for Libraries Not Found issues
2021-09-22
2021-08-11
2021-06024
2021-06-17
CUDA 11.2 installed on
Picotte
2021-05-25
2021-05-21
2021-05-20
2021-05-19
2021-05-12
NFS4 ACLs article created
2021-05-10
Stata 17 has been installed.MUSCLE, URMAP ,
PILER , PILERCR have
been installed
2021-05-06
2021-05-05
2021-04-15
Login to Proteus now requires use of the Drexel VPN
2021-04-06
2021-03-31
2021-03-16
Change coming soon: Proteus access will soon require Drexel VPN (unless on campus)
2021-03-13
2021-03-10
VinaLC 1.3.0 installed on Picotte
2021-03-08
2021-03-04
Three new articles on three common use cases for Slurm:
Picotte Known Issues article
startedSingularity article created, with
examples for non-GPU and GPU containers
2021-03-03
Picotte: GPU and big memory nodes have increased local scratch -
1.7 TB (up from 850 GB)
2021-02-24
Complete BLAST Databases (as of
2021-02-24) have been downloaded to Picotte
SAS installed on Picotte
2021-02-23
NCBI NGS tools installed on Picotte
NCBI BLAST tools installed on Picotte
2021-02-22
Abaqus installed on Picotte
Stata installed on Picotte
2021-02-15
users
2020
2019
2019-10-11:
2019-11-12:
2019-10-25:
NCBI SRA Toolkit 2.10.0 has been
installedSlides from the Proteus User Meetup on Oct 24 are posted
2019-10-16:
2019-10-10:
QIIME - QIIME2 2019.7 has been installed as
a conda env under the module qiime2/2019.8.0
2019-09-13:
Issues with fileserver may not be resolved due to outage at Red
Hat
Default R updated to Microsoft R Open 3.5.1
2019-08-15:
FOAM-extend 4.0 installed
2019-06-11:
High Performance Computing @ Drexel Talk on
Tue Jun 11, 2019 1:30pm Curtis 340
2019-06-06:
2019-05-15:
2019-04-19:
GROMACS 2019.2 has been installed for the
new Skylake nodes
2019-03-13:
Recommended R changed to R/anaconda3 ; R
Studio no longer installed or supported.
2019-03-14:
Quotas for home directories have been activated. If you get the
error message "Disk quota exceeded", you can move your files to
the group directory. See this article for instructions (the
"mv" command will not work): Frequently Encountered Problems
2018
2018-03-08
Anaconda Python (for CPUs only, via the
python/anaconda3 module) has been updated to Python 3.7.1. New
conda environments have been added to it: qiime, biopython,
and pystan.
2018-12-23
Subread has been installedpplacer 1.1.alpha19 has been installed
2018-12-05:
Julia 1.0.2 has been installed
2018-10-29:
Possible fix to mitigate issues raised by jobs using a lot of
memory
2018-09-27:
2018-09-17:
2018-08-15:
Quotas on home directories have been enabled: 15 GiB soft limit,
17 GiB hard limit
For instructions on reproducing your old home directory
structure: [Introduction to Using Proteus
2018-07-13:
2018-07-10:
2018-07-07:
R Studio now available. See the article on
R
2018-07-06:
Caffe
has been updatedKeras deep learning framework has been
installed
2018-07-02:
General information for using the GPU nodes: GPU Jobs . See also examples.
2018-06-15:
NAMD -
instructions for running with charmrunAdded NAMD (ibverbs, smp, CUDA) compilation instructions -
Compiling NAMD
2018-06-08:
GPU nodes are now open for general use. See
2018-06-06:
Where to store data: see Introduction_to_Using_Proteus
2018-05-30:
2018-05-29:
2018-05-25:
2018-05-04:
VinaLC molecular docking software has been
installed
2018-04-09:
ExaBayes bioinformatics software has
been installed
2018-04-06:
GROMACS 2018.1 has been installedVOTCA CSG has been installed
2018-03-22:
SAS statistical software has been installed.
Use is restricted to LeBow College of Business affiliates.
2018-03-19:
BEAGLE (aka beagle-lib) bioinformatics
software has been installed
2018-03-16:
2018-03-01:
Anaconda3 Python has been
installed
2018-02-28:
R 3.4.2 (Intel-only) and 3.4.3 (Microsoft R
Open) have been installed
2018-02-07:
LAMMPS stable-11Aug2017 has been installed
2018-02-01:
Exonerate 2.4.0 (bioinformatics
software) has been installed
2018-01-16:
2018-01-14:
2018-01-12
Updated Vcftools has been installed.
This version is multithreaded, and uses LAPACK for performance
improvements.
2018-01-11
CMAQ 5.2 has been installed
2017
2017-12-15
HDF5 1.10.1 has been installedNetCDF 4.5.0 has been installed
2017-12-02:
2017-11-20:
Kraken 1.0 has been installed
2017-11-09:
2017-11-08
2017-10-18
Instructions for running Jupyter interactively have been posted:
Python#Jupyter
2017-10-16:
2017-10-05:
ADAM 0.22.0 for Apache
Spark 2.x and Scala 2.11 has been
installed
a new ADAM example has been created
2017-10-04:
2017-09-29:
2017-09-25:
Bazel 0.5.4 has been installed
2017-09-21:
MAFFT 7.310 has been installedSPAdes 3.11.0 has been installed
2017-08-23:
2017-08-10:
2017-08-09:
Downtime work is complete.
2017-07-17:
Job Script Example 06 Caffe created
2017-07-09:
Caffe 1.0 deep learning framework
(CPU-only) is now available
2017-06-28:
Python 3.6.1 compiled with both GCC and
Intel ICC is now available
2017-05-25:
Backup Solutions article updated
with information on Google Drive and Microsoft OneDrive
2017-05-23:
Microsoft R Open 3.3.3 (formerly known as
Revolution Analytics R) installed
2017-05-15:
2017-04-10:
2017-03-30
Parallel Environments
article created
2017-03-21:
Workaround for MPI issues found
Updated Matlab article to address
multithreaded processing
2017-03-10:
GROMACS 2016.2 compiled with the Intel
compilers + MKL has been installed
2017-03-08:
Univa Grid Engine has been
updated to version 8.4.4
2017-02-23:
Perl with thread support has been installed.
See the Perl article for details.
2017-02-20:
GroopM with CheckM bioinformatics software
and all dependencies installedvcftools bioinformatics software
installed
2017-02-17:
2017-01-17:
2017-01-11:
2016
2016-11-17:
2016-11-07:
Zlib with CloudFlare optimizations has been
installed.HDF5 compiled with Intel 2015 has been
installedNetCDF compiled with Intel 2015 has been
installed
2016-10-27:
MEGAHIT 1.0.6-hotfix1 bioinformatics
software has been installed
2016-10-21:
IDBA-UD 1.1.3 bioinformatics software has
been installed
2016-10-17:
GroopM with BamM bioinformatics software
have been installed
2016-10-13:
2016-10-12:
Some AMD nodes will be offline in the next few weeks for
hardware reshuffling to accommodate new nodes
2016-10-05:
2016-09-20:
2016-09-19:
Types of Jobs article added
2016-09-16:
pplacer bioinformatics software installed
HMMER bioinformatics software installed
Prodigal bioinformatics software
installed
2016-09-13:
Lustre scratch space will be automatically
cleaned: any files not accessed (incl. read) in >45 days will
be deleted.
2016-09-12:
SortMeRNA has been installed
TeX Live 2016 has been installed
2016-08-31:
Added article List of Online Resources
New software
zstandard -- Facebook's new open
source compression utilityEA-utils -- FASTQ processing
utilities (bioinformatics)
SeqPrep -- program to merge paired
end Illumina reads that are overlapping into a single longer
read (bioinformatics)
2016-08-25:
Issues with wiki search have been resolved.
2016-08-18:
MATLAB license updated to Drexel's new
unlimited license
2016-08-12:
SAMtools with BCFtools 1.3.1 have been
installedPerl 5.24.0 has been installed
2016-07-27:
Matlab R2016a has been installed
2016-07-19:
Stata 14 has been installed
2016-06-16:
Lustre system migration is complete
2016-05-25:
2016-04-21:
Licensed Software article addedMATLAB article updated with information on
license usageAbaqus article updated with information on
license usage
2016-04-13:
Bedtools bioinformatics software has
been installed.MATLAB article updated: added information
on viewing licenses, and more detail on Parallel Computing
Toolbox.
2016-03-14:
2016-03-11:
R 3.2.4 compiled with the Intel toolchain and
liked with optimized linear algebra libraries (MKL) has been
installed.
2016-02-19:
2016-02-15:
FastTree bioinformatics software has
been installed.
2016-01-28:
OpenFOAM computational fluid dynamics
software has been installed.
2016-01-26:
2016-01-19:
MATLAB article updated to include
instructions for using MEX to compile C modules
2016-01-17:
Git 2.7.0 has been installed
2015
2015-12-09:
Wiki updated to MediaWiki 1.26.0
2015-12-01:
CD-Adapco's STAR-CCM+ 10.06.009 has
been installed
2015-11-10:
Git 2.6.3 has been installed.Stata has been installed for LeBow College
of Business affiliates.Backup Solutions article added:
currently only information about using Dropbox is included.
2015-11-09:
2015-10-30:
2015-10-28:
Matlab R2015b is now available
2015-10-23:
2015-10-20:
2015-10-08:
2015-10-05:
Corrected Job Script Example 02 Many Input Files --
index off by one error. Added second example where input files
are named sequentially, but no separate file containing the
filenames is available.
2015-10-01:
Math rendering (use LaTeX as markup) now works, e.g.
G μ ν g μ ν Λ = 8π T μ ν
2015-08-31:
2015-08-28:
2015-08-19:
System-provided Octave 3.4.3 has been removed. In its place,
Octave 4.0.0 has been installed. Use
modulefile "octave/current"
2015-08-11:
2015-08-06:
Big Data Genomics' ADAM 0.17.0 has been installed.
2015-08-04:
Apache Spark 1.4.1 has been installed. Please see Apache Spark article for details.
Interactive GUI applications may be run on compute nodes.
2015-07-24:
Article on OpenMPI updated
with new recommendation. mpirun should be run with the full
path to the executable. This is provided by the MPI_RUN
environment variable.
2015-07-17:
New article added: Lustre Scratch Filesystem
2015-06-30:
2015-06-26:
Matlab R2015a has been installed
2015-06-23:
2015-06-02:
2015-06-01:
2015-05-29:
2015-05-20:
Issue with running namd/intel/2015/openmpi/2.10 resolved.
Issue with MATLAB 2014b toolbox licenses resolved
2015-05-07:
MATLAB GUI again usable from login nodes; to enable this, memory
limit on user processes has been removed - computations
requiring large amounts of memory must be submitted as cluster
jobs
Compiling VASP article updated
2015-05-05:
Global h_rt limit will be reduced to 48 hours this week
Instructions on requesting an interactive session on a compute
node.
2015-04-21:
Added a FAQ
Updated the list
2015-04-14:
NAMD installation updated
2015-04-09:
2015-04-08:
2015-03-25:
The 80 Gbps uplink has been turned on
2015-03-12:
Updated article Recommendations for Jobs
2015-03-03:
Login nodes to be rebooted tonight
Compute nodes will undergo rolling reboots which will not affect
existing jobs
2015-02-13:
2015-01-27:
2015-01-22:
2015-01-12:
If you are using MVAPICH2 with Intel Compilers, please load the
full name of the module:
proteus-mvapich2/intel/64/1.9-mlnx-ofed
2014
2014-12-02:
2014-11-24:
Added article Recommendations for Jobs
2014-11-21:
2014-11-18:
New parallel environments added for getting a specific number of
nodes for multi-node parallel jobs: Writing Job Scripts
2014-11-05:
for Board-related documents
2014-10-15:
2014-10-09:
Wiki now has mobile view
Added info on PuTTY alternatives in Tips for Windows Users
Planned outage - Downtime 2014-10-22
2014-09-04:
David Chin will be out Sep 6 -- Sep 21.
2014-08-28:
2014-07-31:
2014-07-26:
2014-07-24:
2014-07-23:
David Chin will be out most of the day. He will be reachable at
his cellphone number.
2014-07-21:
2014-07-03:
2014-06-30:
POLICY UPDATE Starting 2014-07-15, all jobs will be limited
to 72 hours wallclock duration (h_rt)Users of Intel MPI: Please use the PEs intelmpi or
intelmpi_rr
2014-06-22:
Maintenance shutdown is complete.
2014-06-02:
2014-05-15:
2014-04-28:
Matlab R2014a has been installed.
2014-04-22:
2014-04-16:
ic19n01 is down -- the hard drive needs to be replaced; ETA is
2014-04-17
Started created example job scripts:
2014-04-15:
2014-04-14:
IMPORTANT SECURITY UPDATE Please change your password with
the passwd command on any login node IMMEDIATELY. This is to
address potential data disclosure due to the Heartbleed OpenSSL vulnerability
2014-04-11:
2014-04-03:
Updated Compiling LAMMPS article
to include instructions for compiling with Open64+OpenMPI and
GCC+OpenMPI
2014-04-01:
2014-03-27:
All Intel nodes are back online
Added new parallel environments with round-robin slot
allocation, and for multithread or shared memory parallel
applications: see Writing Job Scripts
Added ability to request exclusive use of compute nodes: see
Writing Job Scripts
2014-03-25
4 Intel nodes down: ic04n03, ic06n03, ic09n03, ic09n04
Simple array job example added Writing Job Scripts
2014-03-20:
2014-03-19:
2014-03-14 (Pi Day special):
Instructions on Compiling Python
2.7.6, and installing it (with example modulefile)
Instructions on installing QIIME
2014-03-11:
Red Hat Developer Toolset 2.1 installed on
login nodes
2014-03-04:
Python 2.7.6, Python 3.3.3 installed --
with numpy, scipy, matplotlib, biopython. Modules are
python/2.7.6 and python/3.3.3Perl 5.18.2 installed -- with BioPerl etc.
Module is perl/5.18.2Mayavi installed on login nodes
2014-02-24:
R 3.0.2 (compiled with gcc) has been installed.
Module is R/3.0.2
2014-02-19:
Grid Engine Scheduler
is being implemented. This changes the way jobs are to be submitted.
2014-02-18:
2014-02-07:
Matlab R2013a installedPreliminary Linpack benchmark (used for TOP500 reckoning) result:
on single Intel node, with Intel compiler + Intel MKL +
Intel MPI -- 288.6 GFLOPS
on single AMD node, with Open64 compiler + ACML w/ FMA4 +
OpenMPI -- 358.0 GFLOPS
on 78 Intel nodes only, with Intel compiler + Intel MKL +
Intel MPI -- 15.06 TFLOPS
multiple AMD nodes -- pending