Informática Aplicada a la Investigación Rotating Header Image

marzo, 2011:

How to send Gaussian

send_gauss command

seend_gauss command submits G09 jobs.

We recommend to use the send_gauss command. This command will prepare the Torque scritp and submit it to the queue. The .log file will remain in the /scratch of the node, but it could be visualized with the remote_vi and remote_molden tools (see bellow).

send_gauss is used as follows:

send_gauss input_file queue_or_walltime core_number [mem] [torque options]

where:

  • input_file: Is the Gaussian input file without the .com extension.
  • queue_or_walltime: Is the walltime in hh:mm:ss format or alternatively select the queue name.
  • ncore_number: Is the core number, it have to be less than 8 or a multiple of 8. It is possible to add node properties, for example 8:itaniumb.
  • mem:  Is the memoru in GB.
  • [torque options]: Advanced option for Torque.

Examples

send_gauss h2o p_slow 8

Will submit the h2o.com job to 8 cores through the p_slow queue, the memory will be set automatically to nproc*900mb, ie, 7200 mb.

send_gauss h2o p_slow 16 20

Will submit the h2o.com job to 2 nodes and 16 cores through the p_slow queue and 20 GB of RAM.

send_gauss h2o 23:00:00 16:xeon 4 ``-m be -M niri@ehu.es -W depend=afterany:4827''

Will submit the h2o.com job to 2 nodes and 16 xeon cores with 23 hours of walltime and 4  GB of RAM. The job will send and email at the beginning and when finishing the job. In addition, it will not start untill job 4827 finish.

qsub interactive command

If qsub is executed without arguments:

qsub

this will ask some questions and send the jobs.

Traditional qsub

We can built our own script for torque. Examples.

Job monitoring

The remote_vi and remote_molden tools allow to watch the .log file and plot it with Molden. For this job have to be submitted with send_gaussian o interactive qsub. It is used as follows

remote_vi 2341
remote_molden 2341

or

remote_vi 2341.arina
remote_molden 2341.arina

where 2341(.arina) is the queue  job id.

Development software

Compilers and installed versions in the different architectures.

Compilers

Xeon
Itanium Opteron
Pendulo
GNU ok ok ok ok
Intel ok ok ok ok
Portlan (PGI) 10.9 10.9
Cuda 3.2
Java Java HotSpot(TM) Server VM (build 1.6.0_03-b05, mixed mode) 

OpenJDK 64-Bit Server VM (build 14.0-b16, mixed mode)

Java JRockit(R) (build R27.6.3-40) Java Java HotSpot(TM) 64-Bit Server VM 

(build 14.0-b16, mixed mode)

HMPP ok

MPI

Xeon
Itanium
Opteron Pendulo
HP-MPI ok ok
Bull-MPI ok ok
Intel MPI ok ok ok
Openmpi ok ok
mvapich2 1.4.1 ok

Libraries

Xeon Itanium
Opteron Pendulo
Intel MKL ok ok ok ok
FFTW ok ok ok ok
GSL ok ok ok ok

ADF

General information

Amsterdam Density Functional (2016.01)

The ADF package is software for first-principles electronic structure calculations. ADF is used by academic and industrial researchers in such diverse fields as pharmacochemistry and materials science. It is particularly popular in the research areas of homogeneous and heterogeneous catalysis, inorganic chemistry, heavy element chemistry, various types of spectroscopy, and biochemistry. Key Benefits of ADF

  • Spectroscopic properties and environments for any type of molecule
  • Excels in transition and heavy metal compounds
  • Accurate, robust, and fast
  • Expert staff and active community
  • Uses Slater functions, beats Gaussians!

ADF can be used for finite systems (molecules) and periodic systems by using ADFBAND. ADF includes graphical interfaces and analysis tools available from Katramila server.

The Service has license for 4 cores.

How to use

To execute the graphical interfaces for input and result visualization use in Katramila:

adfview

To submit an ADF input name input.run created with adfinput program we recommend to use the send_adf

command:

<code>send_adf JOBNAME NODES PROCS[property] TIME MEM [``Otherqueue options'' ]
  • JOBNAME: Input name without the extension
  • NODES: Number of nodes
  • PROCS: Number of processors.
  • TIME: Requested time in hh:mm:ss format.
  • MEM: Memory in GB.
  • [“Otras opciones de Torque”] Other queue oprions.

Example

To submit the au_min2.run input file to 4 processors, with a 20 hours walltime and 4 GB of RAM use

send_adf au_min2.run 1 4 20:00:00 4

More information

ADF web page.

ADF documentation.

 

GROMACS

General information

2018 version. GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.

It is primarily designed for biochemical molecules like proteins, lipids and nucleic acids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. polymers.

How to use

send_gmx

To send gromacs to the queue system  use the send_gmx utility. When executed, shows the command syntax, which is summarized below:

send_gmx ``JOB and Options'' NODES PROCS_PER_NODE TIME MEM [``Other queue options'']
``JOB and Options'': options for the calculation and input of GROMACS name extension. It is very important to keep the quotes.
NODES: Number of nodes.
PROCS: Number of  processors.
TIME: Time requested to the queue system, format hh:mm:ss.
MEM: Memory in Gb.
[``Otras opciones de Torque'' ] There is the possibility to pass more variables to the queuing system.
See examples below.   More information about this options

Examples

We send the gromacs input job1 to 1 node, 4 processors on that node, with a requested time of 4 hours and 1 GB of RAM:

send_gmx ``-s job1.tpr'' 1 4 04:00:00 1

We send job2  to 2 compuation nodes, 8 processors on each node, with a requested time of 192 hours, 8 GB of RAM and to start running after work 1234.arinab is finished:

send_gmx ``-s job2.tpr'' 2 8 192:00:00 8 ``-W depend=afterany:1234'

We  send the input job3 to 4 nodes and 4 processors on each node, with a requested time of 200:00:00 hours, 2 GB of RAM and we request to be send an email at the  beginning and end of the calculation to the direction specified.

send_gmx ``-s  job.tpr'' 4 4 200:00:00 2 ``-m be -M mi.email@ehu.es''

send_gmx command copies the contents of the directory from which the job is sent to /scratch or /gscratch, if we use 2 or more nodes. And there is where the calculation is done.

Jobs Monitoring

To facilitate monitoring and/or control of the gromacs calculations, you can use remote_vi which shows the md.log file (only if it was sent using send_gmx).

More information

http://www.gromacs.org/About_Gromacs

Scientific software

Quantum Mechanics

Katramila
(xeon,rh7,xeon20)
Guinness
(xeon,oxeon)
Kalk2017
(xeon,rh7,xeon28)
Abinit ok ok
ADF 2017.110 2017.110 2017.110
BigDFT ok ok
Casino 2.4 ok
Dirac 08 ok
Espresso ok ok
Gamess Jan 2009 ok
Gaussian 03 & 09 ok ok ok
Jaguar ok ok ok
MIKA .81 ok
NBO 5 ok
NWChem 6.3 ok ok
Orca 3.03  ok ok
PSI4 ok ok
Qbox ok ok
Qsite  ok ok ok
Siesta 2.0.1 ok
Siesta 3.0 ok
TB-LMTO 4.6 ok
Terachem ok
Turbomole 7.0  ok ok
VASP ok ok ok
Wien2K ok ok
Yambo 3.2.2 ok ok

BioChemistry / Molecular Mechanics

Katramila
(xeon,rh7,xeon20)
Guinness
(xeon,oxeon)
Kalk2017
(xeon,rh7,xeon28)
Amber ok ok
DL_POLY ok ok
Gromacs ok ok
Gulp 4.0 ok
LAMMPS ok
Macromodel ok ok ok
NAMD 2.6 ok
Towhee 7.0.2   ok

Mathematics

Katramila
(xeon,rh7,xeon20)
Guinness
(xeon,oxeon)
Kalk2017
(xeon,rh7,xeon28)
Coin-or ok ok
CPLEX ok ok
Grace 5.1.19 ok ok
Mathematica  8.0 ok ok
Matlab ok ok
Matplotlib ok
Octave 3.2.3 ok
Octave 3.2.4 ok
R, RCommander and RStudio 3.3.3 3.3.2 2.7.0
Scilab 5.1.1 ok
Scilab 5.2.2 ok

Genetics

Katramila
(xeon,rh7,xeon20)
Guinness
(xeon,oxeon)
Kalk2017
(xeon,rh7,xeon28)
ABySS ok
BEAST ok ok
BLAST ok
Blast2Go ok
Clean_reads ok
CLUMPP ok
Cufflinks ok
Genepop ok
IDBA-UD ok ok
MetAMOS ok
mpiBLAST ok
QIIME ok
SPAdes ok ok
Structure ok
TopHat ok
Trinity ok
USEARCH ok
Velvet ok

Visualization

Katramila
(xeon,rh7,xeon20)
Guinness
(xeon,oxeon)
Kalk2017
(xeon,rh7,xeon28)
Gaussview ok
Maestro ok ok
Molden ok ok ok
NX client ok
P4VASP ok
x2Go ok ok
XCrysDen ok
Xmakemol  ok ok
VMD ok ok

Other Software

Katramila
(xeon,rh7,xeon20)
Guinness
(xeon,oxeon)
Kalk2017
(xeon,rh7,xeon28)
GAP 4.4 ok
Gretl ok
HTK 3.4.1
NCL-NCAR ok
OOMMF  ok ok
PHENIX ok
SCIPION ok
STAR-CCM+ ok ok ok
WRF 3.1 ok

 

Maestro

General information

Maestro is the unified interface for all Schrödinger software. Impressive rendering capabilities, a powerful selection of analysis tools, and an easy-to-use design combine to make Maestro a versatile modeling environment for all researchers.

In Ginness and Péndulo servers 9.0 version is installed, Maiz has the 8.5 version. We recommend to use Guinness to run Maestro, is the newest server and which support lastest versions.

How to use

Maestro is going to use graphical applications so the researcher must ensure that can open this windows in his computer. How to do this is explained in the access guide of the service.

To execute Maestro run in the terminal

maestro

More information

Maestro web page.

Schrödinger web page.