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Computational Resources

Computational Resources

Arina is composed of 2 subclusters: kalk2020 and kalk2017-katramila

As a whole, Arina features 147 nodes, which provide 196 multicore processors (CPUs) containing a total amount of 4396 cores.

Arina is equiped with two high performance file systems which provide a storage with total net capacity of 120 TB.

Within each subcluster the nodes are connected to each other via an Infiniband network characterized by high bandwith and low latency for intranode communications.

Arina specifics

Subcluster kalk2020

The sublcluster kalk2020 features the following computing nodes:

In total, this set of nodes is composed of 45 computing nodes, which provide 90 multicore processors containing  a total amount of 1800 cores.

This subcluster is endowed with a Parallel Cluster File System (BeeGFS) with a net capacity of 80 TB. Its storage is shared across the entire kalk2020 node compound.

The SLURM queue system is devoted to the management of the jobs submitted to kalk2020.

The intranode communication is speeded up thanks to an infiniband network with a transfer speed up to 100 Gb/s (EDR).

Subcluster kalk2017-katramila

This subcluster includes two sets of computing nodes, namely kalk2017 and katramila.

The kalk2017 node compound is composed of:

In total, it features 68 computing nodes, which provide 136 multicore processors containing  a total amount of 1904 cores.

Each GPU Nvidia Tesla K40m features 2880 GPU cores and 12 GB of integrated GPU RAM.

The katramila node compound is composed of:

In total, it features 34 computing nodes, which provide 70 multicore processors containing  a total amount of 692 cores.

Each GPU Nvidia Tesla K20m features 2496 GPU cores and 5 GB of integrated GPU RAM.

These two sets of computing nodes share a Parallel Cluster File System (Lustre) with a net capacity of 40 TB. Hence, Its storage is shared across the entire node compound of both kalk2017 and katramila.

The TORQUE/MAUI queue system is devoted to the management of the jobs submitted to kalk2017-katramila. Unless otherwise specified in the job submission, the queue system automatically sends jobs to either kalk2017 or katramila computing nodes upon node availability and requested resources.

The intranode communication is speeded up thanks to an infiniband network with a transfer speed up to 56 Gb/s (FDR).

PSI4

Kalkulu Softwarea

General information

PSI4 is an open-source suite of ab initio quantum chemistry programs designed for efficient, high-accuracy simulations of a variety of molecular properties. It is very easy to use and has an optional Python interface.

How to Use

send_psi4

  • To send PSI4 to the queue system use the send_psi4 utility. When executed,
    shows the command syntax, which is summarized below:
  • send_psi4 JOBNAME NODES PROCS_PER_NODE TIME [ MEM ] [``Other queue options'' ]
    JOBNAME: Is the name of the input with extension.
    NODES: Number of nodes.
    PROCS: Number of processors.
    TIME: Time requested to the queue system, format hh:mm:ss.
    MEM: Optional. Memory in Gb ( It will used 1GB/core if not set).
    [``Other Torque Options'' ] Optional. There is the possibility to pass more variables to the queuing system.
    See examples below. More information about this options

More information

PSI4 web page.

VASP

Uncategorized @en

General information

Vienna Ab-initio of Simulation Package

5.4.4 version of the DFT ab-initio program. It uses plane wave basis and pseudopotentials (ultrasoft and PAW-augmented wave method). VSTS tools has been included.

License is needed.

How to use

To usu VASP in parallel is enougth to execute:

/software/bin/vasp

[intlink id=”1353″ type=”post”]p4vasp[/intlink], [intlink id=”5514″ type=”post”]XCrySDen[/intlink] is installed.

v2xsf

Job monitorization

The convergence of a running job can be monitorized with:

remote_vi JOB_ID

that will open the OSZICAR and OUTCAR files in additon to plot the energy and energy variation. It is necessary to use ssh -X or to use X2GO to open the graphic windows.

More information

VASP home page y manuals.

VTST tools.

R, RCommander and RStudio

Genética, Maths, Software de Cálculo

General information

R 3.3.3 is a freely available language and environment for statistical computing and graphics which provides a wide variety of statistical and graphical techniques: linear and nonlinear modelling, statistical tests, time series analysis, classification, clustering, etc. Please consult the R project homepage for further information.

RStudio an RCommander are a graphical front ends for R.

Installed packages

abind, ape, biomformat, cummeRbund, DCGL, DESeq2, DEXSeq, e1071, edgeR, FactoMineR, GEOquery, lavaan, metagenomeSeq, mnormt, optparse, psych, randomForest, Rcmdr, RColorBrewer, ReactomePA, RUVSeq, vegan, WGCNA, xlsx.

Please, ask if you need any more.

How to use it

To use R in the queue scripts execute:

/software/bin/R CMD BATCH  R-input-file.R

to execute RStudio you must connect to Txinparta or Katramila with X2Go and execute

rstudio

to execute RCommander you must connect to Txinparta or Katramila with X2Go and execute R. Then inside R load

library(Rcmdr)

More information

R web page.

rstudio web page.

SCIPION

Uncategorized @en

General information

Scipion is an image processing framework to obtain 3D models of macromolecular complexes using Electron Microscopy. 2016 May version from Github.

How to use

To execute SCIPION use:

/software/bin/scipion

More information

SCIPION web page

AMBER

Uncategorized @en

General information

14 version of AMBER (Assisted Model Building with Energy Refinement) and AMBER-tools15. Program with empiric potentials with molecular dynamics and energy minimization. Especially oriented to the simulation of biological systems.

How to use

The serial and parallel version have been compiled and can be found in the direktory

/software/bin/amber/

send_amber

To send jobs to the queue system you can use the send_amber command:

send_amber "Sander_options" Nodes Procs_Per_Node[property] Time [or Queue] [Mem]  ["Other_queue_options"]

Sander_options: the options you want to use in the calculation, inside quotes
Nodes: is the number of nodes
Procs: is the number of processors (you may uinclude the node type) per node.
Time: or Queue the walltime (in hh:mm:ss format) or the queue name of the calculation
Mem: the PBS memory (in gb)
[Mem] and ["Other_queue_options"] are optional

For “Other queue options” see examples below:

send_amber "sander.MPI -O -i in.md -c crd.md.23 -o file.out" job1 1 8 p_slow
send_amber "sander.MPI -O -i in.md -c crd.md.23 -o file.out" 2 8:xeon vfast 16 "-W depend=afterany:1234"
send_amber "sander.MPI -O -i in.md -c crd.md.23 -o file.out" 4 8 24:00:00 32 "-m be -M mi.email@ehu.es"

More information

Amber home page.

On-line manual.

Tutorials.

 

Qbox

Software @en

General Information

Version: 1.62.3

Qbox is a C++/MPI scalable parallel implementation of first-principles molecular dynamics (FPMD) based on the plane-wave, pseudopotential formalism. Qbox is designed for operation on large parallel computers.

How to use it:

To send qbox jobs to the queue we have created the send_qbox utility_

send_qbox  JOBNAME NODES PROCS_PER_NODE[property] TIME

Executing send_box [Enter] more options will be shown. The program is installed in /software/qbox

More Information

On the Qbox Web page.

IDBA-UD

Genetics, Scientific Software

General information

IDBA-UD 1.1.1 is a iterative De Bruijn Graph De Novo Assembler for Short Reads Sequencing data with Highly Uneven Sequencing Depth. It is an extension of IDBA algorithm. IDBA-UD also iterates from small k to a large k. In each iteration, short and low-depth contigs are removed iteratively with cutoff threshold from low to high to reduce the errors in low-depth and high-depth regions. Paired-end reads are aligned to contigs and assembled locally to generate some missing k-mers in low-depth regions. With these technologies, IDBA-UD can iterate k value of de Bruijn graph to a very large value with less gaps and less branches to form long contigs in both low-depth and high-depth regions.

How to use

To send jobs to the queue you can use the command

send_idba-ud

which after a few questions configures the job.

Performance

IDBA-UD has a good performance and scaling up to 8 cores. Above we did not measure a improvement. In the benchmark the --mimk 40 --step 20 options has been used. When we have decreased the step the the scalling is worse. This trend can be also seen in the second table.

1 core as base 2 cores as base
Cores Time (s) Speed up Performance (%) Speed up Performance (%)
1 480 1 100
2 296 1.6 81 1.0 100
4 188 2.6 64 1.6 79
8 84 5.7 71 3.5 88
12 92 5.2 43 3.2 54

The second benchark has been done with a bigger file with 10 million bases and the  --mink 20 --step 10 --min_support 2 options. We observe a regular behaviour than in the previous benchmark and how the panellization is good up to 4 cores.

Cores Time (s) Speed up Performance
1 13050 1 100
2 6675 2.0 98
4 3849 3.4 85
8 3113 4.2 52
16 2337 5.6 35
20 2409 5.4 27

More information

IDBA-UD web page.

SPAdes

Genetics, Scientific Software, Uncategorized @en

General information

SPAdes 3.6.0 – St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. It works with Illumina or IonTorrent reads and is capable of providing hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. You can also provide additional contigs that will be used as long reads. Supports paired-end reads, mate-pairs and unpaired reads. SPAdes can take as input several paired-end and mate-pair libraries simultaneously. Note, that SPAdes was initially designed for small genomes. It was tested on single-cell and standard bacterial and fungal data sets.

How to use

To send jobs to the queue you can use the

send_spades

command that asks few questions to configure the job.

Performance

We have not measure any performance improvement or time reduction when using several cores in a standard calculation like:

spades.py -pe1-1 file1 -pe1-2 file2 -o outdir

We recommend to use 1 core, unless you know that you can use better performance with several cores.

More information

Web page of SPAdes.

MetAMOS

Genetics, Scientific Software

General information

MetAMOS represents a focused effort to create automated, reproducible, traceable assembly & analysis infused with current best practices and state-of-the-art methods. MetAMOS for input can start with next-generation sequencing reads or assemblies, and as output, produces: assembly reports, genomic scaffolds, open-reading frames, variant motifs, taxonomic or functional annotations, Krona charts and HTML report. 1.5rc3 version.

How to use

To send a job to the queue system there is the

send_metamos

command where you answer a few questions to set up the job. Take into account that MetAMOS use a lot of RAM memory, about 1 GB per million reads.

More information

MetAMOS web page.

QIIME

Genetics, Scientific Software

General information

QIIME (Quantitative Insights Into Microbial Ecology) is an open-source bioinformatics pipeline for performing microbiome analysis from raw DNA sequencing data. QIIME is designed to take users from raw sequencing data generated on the Illumina or other platforms through publication quality graphics and statistics. This includes demultiplexing and quality filtering, OTU picking, taxonomic assignment, and phylogenetic reconstruction, and diversity analyses and visualizations. QIIME has been applied to studies based on billions of sequences from tens of thousands of samples

 How to use

To send QIIME jobs run the command

send_qiime

and answer the questions.

USEARCH

QIIME can use the [intlink id=”7744″ type=”post”]USEARCH[/intlink] pakage.

More information

QIIME home page.

[intlink id=”7700″ type=”post”]USEARCH[/intlink].

 

 

Mathematica

Scientific Software

General Information

Mathematics program that includes symbolic and numeric computing, visualization and programing language. The 10.0 version is installed in Guinness, the 6.0 in the Itanium nodes. Katramila and the newest nodes has the 11.2 version.

Mathematica incluye paralelismo.

Ho to use Mathematica

In interactive mode

The graphical interface can be executed with

mathematica

and the Mathematica console with

math

Nota: If you have problems to visualize the fonts maybe you must install them in your local computer.

In the queue system

In the queue scripts use the line

/software/bin/math < input > output

whre input is the file with the Mathematica commands and output is the file where the output will be saved.

More information

Mathematica home page.

Online documentation.

R-3.2.0

Maths @en

General Information

R is ‘GNU S’, a freely available language and environment for statistical computing and graphics which provides a wide variety of statistical and graphical techniques: linear and nonlinear modelling, statistical tests, time series analysis, classification, clustering, etc. Please consult the R project homepage for further information.

Installed Packages

lavaan, mnormt, psych, Rcmdr, abind, e1071, xlsx, biocLite(),FactoMineR

Please ask if you need any more.

How to use it

To use R-3.2  execute:

/software/R-3.2.0/bin/R CMD BATCH input.R

More Information:

http://cran.r-project.org/

USEARCH

Genetics, Scientific Software

General information

USEARCH is a unique sequence analysis tool that offers search and clustering algorithms that are often orders of magnitude faster than BLAST. We have the free 32 bits version that can not be distributed to third parties and has a 4 GB of RAM limitation.

How to use

To use USEARCH execute

/software/bin/usearch

for example

/software/bin/usearch -cluster_otus data.fa -otus otus.fa -uparseout out.up -relabel OTU_ -sizein -sizeout

USEARCH is only available in the xeon20 type nodes.

QIIME

USEARCH can be use under [intlink id=”7758″ type=”post”]QIIME[/intlink].

More information

USEARCH home page.

[intlink id=”7686″ type=”post”]QIIME[/intlink].

SAMtools, BCFtools and HTSlib 1.2

Genetics, Scientific Software, Software @en

General Information

Samtools is a suite of programs for interacting with high-throughput sequencing data. It consists of three separate repositories:

Samtools
Reading/writing/editing/indexing/viewing SAM/BAM/CRAM format
BCFtools
Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants
HTSlib
A C library for reading/writing high-throughput sequencing data
Samtools and BCFtools both use HTSlib internally, but these source packages contain their own copies of htslib so they can be built independently.

 

How to use It

They are installed in /software/samtools-1.2/, /software/bcftools-1.2/ and  /software/htslib-1.2.1 respectibely.

Something like this should be added in the PBS script.

export PATH=/software/samtools-1.2/bin:/software/bcftools-1.2/bin:$PATH

export LD_LIBRARY_PATH=/software/htslib-1.2.1/lib:$LD_LIBRARY_PATH

 

More Information

http://www.htslib.org/

How to submit siesta jobs

Uncategorized @en

How to submit siesta jobs

There are three ways:

  • Using the send_siesta command.
  • Using qsub in interactive way.
  • With a scritp for the qsub command.

send_siesta

We have written the send_siesta command to submit Siesta jobs. Execute send_siesta and its usage is shownArina. In the following lines we describe it sintax-

send_siesta JOBNAME NODES PROCS_PER_NODE[property] TIME MEM ["Other queue options"]

JOBNAME: Input file without extension.
NODES: Number of nodes to be used.
PROCS_PER_NODE: Cores per node.
TIME: Walltime in hh:mm:ss format.
MEM: Memoria Gb unitatetan.
["Other queue options"]Other instructions to the queue system inside quotes.

Examples
To submit the job1.fdf input in one itaniumb node and for cores:

send_siesta job1 1 4:itaniumb 04:00:00 1

To submit the job2.fdf input to 2 nodes and for cores in each node, 192 hours and 8gb RAM memory. In adition, the job will start after the job with 1234 identifier finish:

send_siesta job2 2 4 192:00:00 8 ``-W depend=afterany:1234''

To submit the job2.fdf input file in 4 nodes and 8 cores per node, 200 hours, eta 15gb RAM. In addition send an email when the jobs starts and finish:

send_siesta job2 4 8 200:00:00 15 ``-m be -M nire.emaila@ehu.es''

The send_siesta command will use the local /scratch directory or the global file system /gscratch depending on the number of nodes used.

 

Interactive qsub

Exekute

qsub

without arguments and answer the question.

Regular qsub

Build a script for qsub,[intlink id=”237″ type=”post”] here there are examples[/intlink], and to execute Siesta use the following line

/software/bin/siesta/siesta_mpi < input.fdf > log.out

Job monitoring

        If you used

send_siesta

        or interactive

qsub

      to submit a job you can monitor it with the following commands:
remote_vi
 It will open the *.out file with gvim.
remote_xmakemol
xmakemol will be used to open the *.ANI file.
remote_qmde
xmgrace will be used to plot energia vs. time in molecular  dynamics simulations.

Examples to monitor the job with 3465 identifier:

remote_vi 3465
remote_xmakemol 3465
remote_qmde 3465

Siesta

Uncategorized @en

General information

Spanish Initiative for Electronic Simulation with Thousands Atoms. DFT based simulation program for solids and molecules. It can be used for molecular dynamics and relaxations. It uses localized orbitals that allow to make calculations with large number of atoms. The academic license is freely distributed but it is necessary to ask for a license. The 3.0rc1 version is installed in the x87_64 nodes and the 2.0.1 in the Itanium nodes.

How to send siesta

[intlink id=”7224″ type=”post”]Follow this link[/intlink].

More information

Siesta home page.

Siesta online manual.

Trinity

Genetics, Scientific Software

General information

2.1.1 release. Trinity, represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data. Trinity combines three independent software modules: Inchworm, Chrysalis, and Butterfly, applied sequentially to process large volumes of RNA-seq reads. Trinity partitions the sequence data into many individual de Bruijn graphs, each representing the transcriptional complexity at at a given gene or locus, and then processes each graph independently to extract full-length splicing isoforms and to tease apart transcripts derived from paralogous genes. Briefly, the process works like so:

  • Inchworm assembles the RNA-seq data into the unique sequences of transcripts, often generating full-length transcripts for a dominant isoform, but then reports just the unique portions of alternatively spliced transcripts.
  • Chrysalis clusters the Inchworm contigs into clusters and constructs complete de Bruijn graphs for each cluster. Each cluster represents the full transcriptonal complexity for a given gene (or sets of genes that share sequences in common). Chrysalis then partitions the full read set among these disjoint graphs.
  • Butterfly then processes the individual graphs in parallel, tracing the paths that reads and pairs of reads take within the graph, ultimately reporting full-length transcripts for alternatively spliced isoforms, and teasing apart transcripts that corresponds to paralogous genes.

How to use

You can use the

send_trinity

command to submit jobs to the queue system. After answering few questions a script will be created and submitted to the queue system. For advanced users it can be used to generate a sample script.

Performance

Trinity can be run in parallel but it is not very efficient above 4 cores with low performance, as can be seen in the the table. Trinity consumes high amounts of RAM.

Performance of Trinity
Cores  1 4 8 12
Time 5189 2116 1754 1852
Speddup 1 2.45 2.96 2.80
Efficiency (%)  100 61 37 23

 

More information

Trinity web page.

PHENIX

Software @en

General information

Versión dev-2229 (higher than 1.10) of PHENIX (Python-based Hierarchical ENvironment for Integrated Xtallography). PHENIX is a software suite for the automated determination of macromolecular structures using X-ray crystallography and other methods. It is ready to use with [intlink id=”1969″ type=”post”]AMBER[/intlink].

How to use

To execute the graphical interface in Guinness execute the command:

phenix &

To execute PHENIX in the queue system scripts the PHENIX working environment must be loaded first with the source command. Execute for example:

phenix.xtriage my_data.sca [options]

More information

PHENIX web page.
Online documentation.
Documentation in pdf.

FFTW libraries

Development software

Fastest Fourier Transform in the West to make all type of Fourier transforms.

The 3.3.3 version is installed in /software/fftw. Several types have been compiled (threads, simple precission,etc)

To link them use

-L/software/fftw -lfftw3

If you have doubts ask the technicians.

More information in the web page FFTW.

Abinit

Quantum Mechanics @en, Scientific Software

General Information

ABINIT is a package whose main program allows one to find the total energy, charge density and electronic structure of systems made of electrons and nuclei (molecules and periodic solids) within Density Functional Theory (DFT), using pseudopotentials and a planewave or wavelet basis. ABINIT also includes options to optimize the geometry according to the DFT forces and stresses, or to perform molecular dynamics simulations using these forces, or to generate dynamical matrices, Born effective charges, and dielectric tensors, based on Density-Functional Perturbation Theory, and many more properties. Excited states can be computed within the Many-Body Perturbation Theory (the GW approximation and the Bethe-Salpeter equation), and Time-Dependent Density Functional Theory (for molecules). In addition to the main ABINIT code, different utility programs are provided.  netcdf, bigdft, wannier90, etsf_io, libxc, etc. plugins are included. 7.0.4 version is installed.

How to send Abinit

The programs are in /software/bin/abinit. For instance, to execute abinit in the queue system scripts use

/software/bin/abinit/abinit < input.files > out.log

Depending on the number of cores asked to the queue system it will execute in parallel. The jobs can be also submitted with the [intlink id=”233″ type=”post”]interactive qsub[/intlink] command.

There are other utilities like aim, anaddb, band2eps, conducti, cut3d, lwf, macroave, mrgddb, mrggkk, newsp, optic, etc.

Benchmark

We have made a small benchmark with the 6.12.3 version.

System 1 cores 4 cores 8 cores
Xeon12 7218 2129 1045
Xeon8 7275 1918 1165
Itanium 8018 2082 1491
Opteron 17162 4877 2802

We observe that Abinit works fine in itanium and xeon nodes while in opteron nodes is slower.

More information

Abinit web page.

Online manuals.

Internal User Rates

Rates

General Information

The internal rate applies to researchers and centers of the UPV / EHU. Includes service and applications. The rates will be valid from 15-09-2021 to  14-09-2022.

CPU usage charges

The fee for a research group will be 0.005 € / hour and core.

Storage Rates

Every user has a 3 gb  storage quota taht will not be charged. Having more data in Arina will be charged as follows:

Rates for extra GB stored each month
CPU usage Range Storage Fee
(in days per year) (€/Gb) per month
2500< cpu 0.1
100< cpu <2500 0.5
1< cpu <100 1.0
0< cpu <1 1.5

CPU usage charges until 08-31-2019

The fee for a research group will be:

  1. 0.011 € / hour and core until the group reaches the use of 18.939,39 days of calculation (corresponding to 5.000 €).
  2. Once this consumption is reached , the rest of the computing time will be charged at 0.003€ / hour and core.

ABySS

Genetics, Scientific Software

General Information

1.3.2 version of ABySS (Assembly By Short Sequences). ABySS is a de novo, parallel, paired-end sequence assembler that is designed for short reads. ABySS can be executed in parallel.

See also the installed [intlink id=”6043″ type=”post”]velvet[/intlink] and comparing both we have published article.

How to use

The executables can be found in /software/abyss/bin. To run abyss in a script type in it:

/software/abyss/bin/abyss-pe [abyss-pe options]

Performance

See also the installed [intlink id=”6043″ type=”post”]velvet[/intlink] and comparing both we have published article.

Parallelization

Some benchmarks has been performed with ABySS. They have been performed using file from an Illumina HiSeq2000 NGS with 100 bp per sequence. In the table 1 we can see an example about how ABySS scales as a function of the number of cores. As we can see ABySS scales very up to 8 cores. The results is valid unless for more than 10e6 sequences.

Table 1. Execution time of abyss-pe in seconds as a function the number of cores
cores 2 4 8 12 24
Time (s) 47798 27852 16874 14591 18633
Aceleration 1 1.7 2.8 3.3 2.6
Performance(%) 100 86 71 55 21

Execution time

We have analized as well the execution time as a function of the size of the data. In the table 2 we  observe how from 1 million to 10 millions of sequences the execution time increases by 10 as well. From 10 to 100 millions of sequences the time increases a little more, between 10 t0 20. Therefore, the behavior is more or less lineal.

Table 2. Execution time in seconds of abyss-pe executed in 2, 4 y 8 cores as a function of the number of processed sequences.
sequences 10e6 10e7 10e8
Time in 2 cores (s) 247 2620 47798
Time in 4 cores (s) 134 1437 27852
Time in 8 cores (s) 103 923 16874

RAM memory

In these kind of programs more important than the execution time, which is reasonable, is the RAM memory usage, which can limit the calculation type. In the table 3 we observe how the RAM increases as a function of the number of sequences. We also show the logarithms of the measured values which has been used for a lineal regression. The jobs has been performed in 12 cores.

Tabl3 3. RAM memory used by abyss-pe as a function of the number of processed sequences. The logarithms of the measured values are also shown.
sequences 10e6 5*10e6 10e7 5*10e7 10e8
RAM (GB) 4.0 7.6 11 29 44
log(sequences) 6 6.7 7 7.7 8
log(RAM) 0.60 0.88 1.03 1.46 1.65

From the values of the table we obtain a fitting of the RAM in GB as a function of the number of sequences (s) to the equation

log(RAM)=0.53*log(s)-2.65

o equivalently

RAM=(s^0.53)/447

Conclusion

The memory usage is smaller than in other assemblers like [intlink id=”6043″ type=”post”]Velvet[/intlink], see as well the report Velvet performance in the machines of the Computing Service of the UPV/EHU and comparing both we have published article. In addition, the parallelization with MPI of ABySS allows to aggregate the RAM memory of several nodes to perform larger calculations.

More information

ABySS web page.
[intlink id=”6043″ type=”post”]Velvet[/intlink] assembler.
Velvet performance in the machines of the Computing Service of the UPV/EHU report.

Velvet and ABySS performance in the machines of the Computing Service of the UPV/EHU, post in the hpc blog.

abyss-pe

Clean reads

Genetics, Scientific Software

General information

0.2.2 Version. clean_reads cleans NGS (Sanger, 454, Illumina and solid) reads. It can trim:

  • bad quality regions
  • adaptors
  • vectors
  • regular expresssions

It also filters out the reads that do not meet a minimum quality criteria based on the sequence length and the mean quality. It can run in parallel.

Ho to use

To submit clean_reads jobs to the queue system execute the command

send_clean_reads

It will ask few questions to build the script and submit it to the queue.

Performance

clean_reads can be executed in parallel and scales well up to 8 cores. For 12 cores the performance is very poor. In the table 1 we show the results of the benchmark. They have been executed in a 12 cores node with E5645 Xeon processors.

Execution time in seconds as a function of the number of cores
cores 1 4 8 12
Time (s) 1600 422 246 238
Speedup 1 3.8 6.5 6.7
Performance (%) 100 95 81 56

The used command has been

clean_reads -i in.fastq -o out.fastq -p illumina -f fastq -g fastq -a a.fna -d UniVec -n 20 --qual_threshold=20 --only_3_end False -m 60 -t 12

More information

clean_reads web page.

Velvet

Genetics, Scientific Software

General information

1.2.03 version. Velvet is a set of algorithms manipulating de Bruijn graphs for genomic and de novo transcriptomic Sequence assembly. It was designed for short read sequencing technologies, such as Solexa or 454 Sequencing and was developed by Daniel Zerbino and Ewan Birney at the European Bioinformatics Institute. The tool takes in short read sequences, removes errors then produces high quality unique contigs. It then uses paired-end read and long read information, when available, to retrieve the repeated areas between contigs.

See also the installed [intlink id=”6200″ type=”post”]ABySS[/intlink] and comparing both we have published article.

How to use

To run velveth or velvetg add in your scripts for the Torque queue system the corresponding command:

/software/bin/velvet/velveth [velvet options]
/software/bin/velvet/velvetg [velvet option]

Performance

Velvet has been compiled with parallel support througth OpenMP. We have measured the perfomance and the results are available in the report about the Velvet performance in the machines of the Computing Service of the UPV/EHU. Velvet uses huge amount of RAM for large calculations and we have measured it. In the report some simple formulas are obtained to predict the use of RAM for their input files, so the researches can know the needed RAM before start the calculations and in this way can plan their research.

See also the installed [intlink id=”6200″ type=”post”]ABySS[/intlink] and comparing both we have published article.

More information

Velvet web page.
Velvet performance in the machines of the Computing Service of the UPV/EHU report.
Velvet and ABySS performance in the machines of the Computing Service of the UPV/EHU, post in the hpc blog.

BLAST

Genetics, Scientific Software

General Information

2.2.24 version of BLAST de NCBI. Due to performance reasons it has not been installed in Itanium nodes.

 

Data bases

The Service has installed several data bases, contact the technicians to use them or install new ones.

How to use

To submit jobs to the queue system we strongly recomend to use the command

send_blast

it will make some questions to prepare the job

Performance and gpuBLAST

We have compared BLAST with mpiBLAST and gpuBLAST, the result of the bechmarks are in the blog of Service. [intlink id=”1495″ type=”post” target=”_blank”]mpiBLAST[/intlink] is installed in the Service.

 

More information

BLAST web page.

[intlink id=”1493″ type=”post”]Blast2GO[/intlink] y [intlink id=”1495″ type=”post” target=”_blank”]mpiBLAST[/intlink] is also installed.

Genepop

Genetics, Scientific Software

General information

4.1 version.

Genepop is a population genetics software package, which has options for the following analysis: Hardy Weinberg equilibrium, Linkage Disequilibrium, Population Differentiation, Effective number of migrants, Fst or other correlations.

How to use

To execute Genepop in the queue system you must include in the script of the queue system:

/software/bin/Genepop < input_file

where input_file has the options for Genepop, i.e., the answer to Genepop when it runs in interactive mode. We recommend to use [intlink id=”233″ type=”post”]qsub in interactive mode[/intlink] to submit the jobs

 

More information

Genepop web page.

CLUMPP

Genetics, Scientific Software

General information

1.1.3 version. CLUMPP is a program that deals with label switching and multimodality problems in population-genetic cluster analyses. CLUMPP permutes the clusters output by independent runs of clustering programs such as [intlink id=”5875″ type=”post”]structure[/intlink], so that they match up as closely as possible. The user has the option of choosing one of three algorithms for aligning replicates, with a tradeoff of speed and similarity to the optimal alignment.

How to use

To execute CLUMPP in the queue system you must include in the script of the queue system:

/software/bin/CLUMPP

with the corresponding options of structure. We recommend to use [intlink id=”233″ type=”post”]qsub in interactive mode[/intlink] to submit the jobs

 

More information

CLUMPP web page.

Structure

Genetics, Scientific Software

General information

2.33 version.

The program structure is a free software package for using multi-locus genotype data to investigate population structure. Its uses include inferring the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed. It can be applied to most of the commonly-used genetic markers, including SNPS, microsatellites, RFLPs and AFLPs.

How to use

To execute the graphical user interface execute in Péndulo, Maiz or Guinness

structure

To execute graphical applications read [intlink id=”48″ type=”post”]how to connect to Arina[/intlink].

To execute structure in the queue system you must include in the script of the queue system:

/software/bin/structure

with the corresponding options of structure. We recommend to use [intlink id=”233″ type=”post”]qsub in interactive mode[/intlink] to submit the jobs

 

More information

Structure web page.

MCCCS Towhee 7.0.2

Biochemistry, Scientific Software, Software @en

Towhee is a Monte Carlo molecular simulation code originally designed for the prediction of fluid phase equilibria using atom-based force fields and the Gibbs ensemble with particular attention paid to algorithms addressing molecule conformation sampling. The code has subsequently been extended to several ensembles, many different force fields, and solid (or at least porous) phases.

General Information

Towhee serves as a useful tool for the molecular simulation community and allows science to move forward more quickly by eliminating the need for individual research groups to rewrite routines that already exist and instead allows them to focus on algorithm advancement, force field development, and application to interesting systems.

Towhee may use different type of ensembles and Monte Carlo moves implemented into Towhee and can alos used different  force fields included with the distribution. (See here for more information )

How to Use

send_towhee

  • To send Towhee to the queue system  use the send_gulp utility. When executed,
    shows the command syntax, which is summarized below:
  • send_towhee JOBNAME NODES PROCS_PER_NODE TIME [ MEM ] [``Other queue options'' ]
JOBNAME: Is the  name of the Output.
NODES: Number of nodes.
PROCS: Number of  processors.
TIME: Time requested to the queue system, format hh:mm:ss.
MEM: Optional. Memory in Gb ( It will used 1GB/core if not set).
[``Other Torque Options'' ] Optional. There is the possibility to pass more variables to the queuing system.
See examples below.   More information about this options

Examples

We send a Towhee job1 to 1 node, 4 processors on that node, with a requested time of 4 hours . The results will be in the OUT file.

send_towhee OUT 1 4 04:00:00

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_towhee OUT 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 arequested 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_towhee OUT 4 4 200:00:00 2 ``-m be -M mi.email@ehu.es''

send_towhee 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 Towhee calculations, you can use remote_vi

remote_vi JOBID

It show us the *.out file  (only if it was sent using send_towhee).

More information

http://towhee.sourceforge.net/

Gulp 4.0

Biochemistry

General Information

GULP is a program for performing a variety of types of simulation on materials using boundary conditions of 0-D (molecules and clusters), 1-D (polymers), 2-D (surfaces, slabs and grain boundaries), or 3-D (periodic solids). The focus of the code is on analytical solutions, through the use of lattice dynamics, where possible, rather than on molecular dynamics. A variety of force fields can be used within GULP spanning the shell model for ionic materials, molecular mechanics for organic systems, the embedded atom model for metals and the reactive REBO potential for hydrocarbons. Analytic derivatives are included up to at least second order for most force fields, and to third order for many.

How to Use

First, before you use it, be aware of its usage conditions.

send_gulp

  • To send GULP to the queue system  use the send_gulp utility. When executed,
    shows the command syntax, which is summarized below:
  • send_gulp JOBNAME NODES PROCS_PER_NODE TIME [ MEM ] [``Other queue options'' ]
JOBNAME: Is the  name of the input with extension.
NODES: Number of nodes.
PROCS: Number of  processors.
TIME: Time requested to the queue system, format hh:mm:ss.
MEM: Optional. Memory in Gb ( It will used 1GB/core if not set).
[``Other Torque Options'' ] Optional. There is the possibility to pass more variables to the queuing system.
See examples below.   More information about this options

Examples

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

send_gulp job1.gin 1 4 04:00:00

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_gulp job2.gin 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 arequested 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_gulp job.gin 4 4 200:00:00 2 ``-m be -M mi.email@ehu.es''

send_gulp 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 GULP calculations, you can use remote_vi

remote_vi JOBID

It show us the *.out file  (only if it was sent using send_lmp).

More information

http://projects.ivec.org/gulp/

LAMMPS

Biochemistry, MM/MD @en, Software @en

LAMMPS (“Large-scale Atomic/Molecular Massively Parallel Simulator”) is a molecular dynamics program from Sandia National Laboratories. LAMMPS makes use of MPI for parallel communication and is a free open-source code, distributed under the terms of the GNU General Public License.
LAMMPS was originally developed under a Cooperative Research and Development Agreement (CRADA) between two laboratories from United States Department of Energy and three other laboratories from private sector firms. It is currently maintained and distributed by researchers at the Sandia National Laboratories. (Taken from Wikipedia). Jun-05-2019 version.

General Information

LAMMPS is a classical molecular dynamics code that models an ensemble of particles in a liquid, solid, or gaseous state. It can model atomic, polymeric, biological, metallic, granular, and coarse-grained systems using a variety of force fields and boundary conditions.

In the most general sense, LAMMPS integrates Newton’s equations of motion for collections of atoms, molecules, or macroscopic particles that interact via short- or long-range forces with a variety of initial and/or boundary conditions. For computational efficiency LAMMPS uses neighbor lists to keep track of nearby particles. The lists are optimized for systems with particles that are repulsive at short distances, so that the local density of particles never becomes too large. On parallel machines, LAMMPS uses spatial-decomposition techniques to partition the simulation domain into small 3d sub-domains, one of which is assigned to each processor. Processors communicate and store “ghost” atom information for atoms that border their sub-domain. LAMMPS is most efficient (in a parallel sense) for systems whose particles fill a 3d rectangular box with roughly uniform density. Papers with technical details of the algorithms used in LAMMPS are listed in this section.

How to Use

send_lmp

  • To send LAMMPS to the queue system  use the send_lmp utility. When executed,
    shows the command syntax, which is summarized below:
  • send_lmp JOBNAME NODES PROCS_PER_NODE TIME [ MEM ] [``Other queue options'' ]
    JOBNAME: Is the  name of the input with extension.
    NODES: Number of nodes.
    PROCS: Number of  processors.
    TIME: Time requested to the queue system, format hh:mm:ss.
    MEM: Optional. Memory in Gb ( It will used 1GB/core if not set).
    [``Other Torque Options'' ] Optional. There is the possibility to pass more variables to the queuing system.
    See examples below.   More information about this options

Examples

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

send_lmp job1.in 1 4 04:00:00

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_lmp job2.inp 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 arequested 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_lmp job.tpr 4 4 200:00:00 2 ``-m be -M mi.email@ehu.es''

send_lmp 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 LAMMPS calculations, you can use remote_vi

remote_vi JOBID

It show us the *.out file  (only if it was sent using send_lmp).

More information

http://lammps.sandia.gov

GRETL

Scientific Software

General information

Gretl (Gnu Regression, Econometrics and Time-series Library) is a software for econometric analysis. 1.9.6 version is installed.

Charateristics

  • Incluye una gran variedad de estimadores: mínimos cuadrados, máxima verosimilitud, GMM; de una sola ecuación y de sistemas de ecuaciones
  • Métodos de series temporales: ARMA, GARCH, VARs y VECMs, contrastes de raíces unitarias y de cointegración, etc.
  • Variables dependientes limitadas: logit, probit, tobit, regresión por intervalos, modelos para datos de conteo y de duración, etc.
  • Los resultados de los modelos se pueden guardar como ficheros LaTeX, en formato tabular y/o de ecuación.
  • Incluye un lenguaje de programación vía ‘scripts’ (guiones de instrucciones): las órdenes se pueden introducir por medio de los menús o por medio de guiones.
  • Estructura de bucles de instrucciones para simulaciones de Monte Carlo y procedimientos de estimación iterativos.
  • Controlador gráfico mediante menús, para el ajuste fino de los gráficos Gnuplot.
  • Enlace a GNU R, GNU Octave y Ox para análisis más sofisticados de los datos.

How to use

In order to use Gretl execute

/software/bin/gretlcli

More information

Gretl web page.

HMPP

Development software

General information

Based on C and FORTRAN directives, HMPP Workbench version 2.5.2 offers a high level abstraction for  GPGPUs. HMPP compiler integrates powerful data-parallel backends for NVIDIA CUDA and OpenCL. The HMPP runtime ensures application deployment on multi-GPU systems.

How to use

In order to execute the compiler use

hmpp

for example, to compile the test.c program by using the gcc compiler use

hmpp gcc test.c -o test

More information

HMPP web page

Gaussview

Software @en, Visualization

5.0.9 version of Gaussview, GUI to create and analyze [intlink id=”12″ type=”post”]Gaussian[/intlink] jobs. In order to use it, execute:

gv

We strongly recommend to use it through an NX-client in Guinness. You can find information about how to configure NX-client correctly in the  following step by step guide.

CPLEX

Maths @en, Scientific Software

General information

IBM ILOG CPLEX Optimizer’s mathematical optimization technology enables smarter decision-making for efficient resource utilization. CPLEX provides robust algorithms for demanding problems: IBM ILOG CPLEX Optimizer has solved problems with millions of constraints and variables. 12.6.3 version.

Features

  • Automatic and dynamic algorithm parameter control
    IBM ILOG CPLEX Optimizer automatically determines “smart” settings for a wide range of algorithm parameters, usually resulting in optimal linear programming solution performance. However, for a more hands-on approach, dozens of parameters may be manually adjusted, including algorithmic strategy controls, output information controls, optimization duration limits, and numerical tolerances.
  • Fast, automatic restarts from an advanced basis
    Large problems can be modified, and then solved again in a fraction of the original solution time.
  • A variety of problem modification options, such as:
    – The ability to add and delete variables
    – The ability to add and delete constraints
    – The ability to modify objective, right-hand side, bound and matrix coefficients
    – The ability to change constraint types
  • A wide variety of input/output options, such as:
    – Problem files: read/write MPS files, IBM ILOG CPLEX Optimizer LP files, MPS basis and revise files, binary problem/basis files
    – Log files: session information and various solution reports
    – Solution files: ASCII and binary solution files
    – IBM ILOG CPLEX Optimizer messages: Each message type (such as RESULTS, WARNINGS or ERRORS) can be directed to specified files, or completely suppressed.
  • Post solution information and analysis, including:
    – Objective function value
    – Solution variable and slack values
    – Constraint dual values (shadow prices)
    – Variable reduced costs
    – Right-hand side, objective function, and bound sensitivity ranges
    – Basic variables and constraints
    – Solution infeasibilities (if any exist)
    – Iteration/node count, solution time, process data
    – Infeasibility (IIS) finder for diagnosing problem infeasibilities
    – Feasibility optimizer for automatic correction of infeasible models

How to use

To use CPLEX execute:

/software/bin/cplex/cplex

Benchmark

There is a small benchmark usingCOIN-OR, see [intlink id=”5224″ type=”post”]COIN-OR web page[/intlink].

More information

CPLEX web page.

COIN-OR

Maths @en, Scientific Software

General information

1.7.5 version. The Computational Infrastructure for Operations Research (COIN-OR**, or simply COIN) project is an initiative to spur the development of open-source software for the operations research community. It has been konpiled using [intlink id=”5240″ type=”post”]CPLEX[/intlink].

How to use

The blis, cbc, clp, OSSolverService and symphony executables are installed in /software/bin/CoinAll. To use, for example, clp execute in the torque scripts:

/software/bin/CoinAll/clp

More information

Coin-or home page.

DL_POLY

Biochemistry, Scientific Software

General information

4.02 version of the MD program for macromolecules, polymers, ionic systems, solutions and other molecular systems. Developed at the Daresbury Laboratory. In Pendulo the 2.2 version remains. There is already the DL_POLY_CLASSIC version which currently is not been developed.

How to submit to the queue

The program is installed in all the architectures, Arina and Pendulo (DL_POLY 2.2). To execute it include in the scripts:

/software/bin/DL_POLY/DL_POLY.Z

The program will exekute in GPGPUs if it starts in these kind of nodes. Besides, they can be selected by using the gpu label within [intlink id=”244″ type=”post”]the queue system[/intlink].

The GUI is also installed. To execute it use:

/software/bin/DL_POLY/gui

Some utilities has been installed in the /software/bin/DL_POLY/ directory.

Benchmark

We show a small benchmarks performed with dl_ploly_4.02. We stady the parallelization as well as the performance of the GPGPUs.

System 1 cores 4 cores 8 cores 16 cores 32 cores 64 cores
Itanium 1.6 GHz 1500 419 248 149 92 61
Opteron 1230 503 264 166 74
Xeon 2.27 GHz 807 227 126 67 37 25

We show in the firs benchamrk that DL_POLY scales very well and that the xeon nodes are the fastest ones, so we recomend them for large jobs.

System 1 cores 2 cores 4 cores 8 cores 16 cores 32 cores
Itanium 1.6 GHz 2137 303 165 93 47
Opteron 1592 482 177 134 55
Xeon 2.27 GHz 848 180 92 48 28
1 GPGPU 125 114 104 102
2 GPGPU 77 72 69
4 GPGPU 53 50
8 GPGPU 37
System 1 cores 2 cores 4 cores 8 cores 16 cores 32 cores 64 cores
Xeon 2.27 GHz 2918 774 411 223 122 71
1 GPGPU 362 333 338 337
2 GPGPU 240 222 220
4 GPGPU 145 142
8 GPGPU 97

We show that the GPGPUs speedup the calculation but each time we double the number of GPGPUs the speed up is multiplied but only 1.5. Because of this for large number of GPGPUs or cores is better to use the paralelization over cores. For example, one node has 8 cores and 2 GPGPUS. The 2 GPGPUs need 220 s while 8 cores need 411 s. Still 4 GPGPUs are faster than 16 cores but 32 cores with 71 s are faster than 8 GPGPUs that need 97 s. Therefore, the GPGPUS can speedup jobs in PCs or single nodes, but for jobs that require higher parallelization the cores parallelization is more effective.

DL_POLY is designed for big systems and the use up to thousand of cores. According to the documentation:

The DL_POLY_4 parallel performance and efficiency are considered very-good-to-excellent as long as (i) all CPU cores are loaded
with no less than 500 particles each and (ii) the major linked cells algorithm has no dimension less than 4.

More information

DL_POLY web page.

DL_POLY user guide (pdf).

DL_POLY GUI user guide (pdf).

Espresso

Job Submission

General information

opEn-SourceP ackage for Research in Electronic Structure, Simulation, and Optimization

ESPRESSO is an integrated suite of computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials (both norm-conserving and ultrasoft).

The 6.1 version is availabe.  The home page of the code is in  DEMOCRITOS National Simulation Center of the Italian INFM.

Quantum ESPRESSO builds onto newly-restructured electronic-structure codes (PWscf, PHONON, CP90, FPMD, Wannier) that have been developed and tested by some of the original authors of novel electronic-structure algorithms – from Car-Parrinello molecular dynamics to density-functional perturbation theory – and applied in the last twenty years by some of the leading materials modeling groups worldwide. Innovation and efficiency is still our main focus.

How to use

[intlink id=”4795″ type=”post”] See how to send espresso  section.[/intlink]

Monitorization

  • remote_vi: Shows the *.out file of espresso.
  • myjobs: During the execution of a job it shows the CPU and memory (SIZE) usage.

Benchmark

We show various benchmarks results for  ph.x and pw.xy in our  service the machines. The best are the Xeon nodes and scale well up to 32 cores. Notice that the communication network in the  Xeon nodes is better.

Tabla 1:Execution times pw.x (4.2.1 version).
System 8 cores 16 cores 32 cores
Xeon 1405 709 378
Itanium2 2614 1368 858
Opteron 2.4 4320 2020 1174
Core2duo 2.1 – – –
Tabla 2: Execution times ph.x (versión 4.2.1)
System 8 cores 16 cores 32 cores
Xeon 2504 1348 809
Itanium2 2968 1934 1391
Opteron 2.4 6240 3501 2033
Core2duo 2.1 – – –

More information

ESPRESSO Web page.

On Line Documentation.

ESPRESSO Wiki.

send_espresso

Job Submission

send_espresso

To launch espresso calculations to the queue system the send_espresso script is available. Executing it, send_espresso [Enter], the syntax of the command is shown:

send_espresso input Executable Nodes Procs_per_node Time Mem [``Otherqueue options'' ]
Input Name of the espresso input file without extension
Executable Name of the espresso program you want to use: pw.x, ph.x, cp.x,…
Nodos Number of nodes
Procs_per_node: Is the number of processors per node
Time: The walltime (in hh:mm:ss format) or the queue name
Mem Memory in  GB (without the unit)
[“Otras opciones de Torque”] See example bellow

Examples

Example1: send_espresso job1 pw.x 1 4 04:00:00 1
Example2: send_espresso job2 cp.x 2 4 192:00:00 8 "-W depend=afterany:1234"
Example3: send_espresso job5 pw.x 4 8 192:00:00 8 "-m bea -M email@adress.com"

Traditional way

The executables can be found in /software/Espresso, for instance to execute pw.x in queue script use

source /software/Espresso/compilervars.sh
/software/Espresso/bin/pw.x -npool ncores < input_file > output_file
In the -npool ncores option substitute ncores by the number of cores of the job.

How to send Turbomole

Software @en

send_turbo

To launch turbomole calculations to the queue system send_turbo is available. Executing it, send_turbo without arguments the syntax of the command and examples are shown:

send_turbo "EXEC and Options" JOBNAME TIME[or QUEUE] PROCS[property]  MEM [``Other queue options'' ]

  • EXEC: Name of the Turbomole program you wnat to use.
  • JOBNAME: Name of the Turbomole control file (usually control).
  • PROCS: is the number of processors (you can not include the node type).
  • TIME[or QUEUE]: the walltime (in hh:mm:ss format) or the queue name.
  • MEM: memory in  GB (without the unit).
  • [“Other queue options”]  see examples below.

Examples

To run Turbomole (jobex) with the control input file in 8 cores and 1 GB of RAM execute:

send_turbo jobex control 04:00:00 8 1

To run Turbomole (jobex -ri) with the control input file in 16 cores, 8 GB of RAM and after 1234 job has finished execute:

send_turbo jobex -ri control 192:00:00 16 8 ``-W depend=afterany:1234''

Turbomole

Software @en

Presently TURBOMOLE is one of the fastest and most stable codes available for standard quantum chemical applications. Unlike many other programs, the main focus in the development of TURBOMOLE has not been to implement all new methods and functionals, but to provide a fast and stable code which is able to treat molecules of industrial relevance at reasonable time and memory requirements.

General information

TURBOMOLE is used by academic and industrial researchers. It is used in research areas ranging form homogeneous and heterogeneous catalysis, inorganic and organic chemistry to various types of spectroscopy, and biochemistry. The philosophy behind the development of the code was, and still is, its usefulness for applications.
It provides:
  • all standard and state of the art methods for ground state calculations (Hartree-Fock, DFT, MP2, CCSD(T))
  • excited state calculations at different levels (full RPA, TDDFT, CIS(D), CC2, ADC(2), …)
  • geometry optimizations, transition state searches, molecular dynamics calculations
  • various properties and spectra (IR, UV/Vis, Raman, CD)
  • fast and reliable code, approximations like RI are used to speed-up the calculations without introducing uncontrollable or unkown errors
  • parallel version for almost all kind of jobs
  • free graphical user interface

How to use it

The programme is in  guinness at /software/TURBOMOLE.We have created the send_turbo script to facilitate the way to send turbomole calculations to the queue. See [intlink id=”4755″ type=”post”]How to send Turbomole[/intlink].

TmoleX,  is also available, to help the input creationd and analisys of the results. There is a free download of TmoleX that you can install in your PC or it is available on Guinness. To use TmoleX execute:

TmoleX

To cleanly stop a job after the current iteration, for example the 1234.arina job, use the command:

turbomole_stop 1234

Remember to delete the “stop” file in the directory if you want to resubmit the calculation.

More Infromation

Turbomole web page.

Turbomole Manual

Turbomole Tutorial

OOMMF

Uncategorized @en

General information

1.2 version of the micromagnetic simulation program. It has not been compiled with the parallel version of tcl.

How to use

By executing

oommf.tcl

GUI will appear to prepare and analize calculations. To submit OOMMF to the queue system you can execute

send_oommf

which will build a correct script and submit it.

Benchmark

A small benchmark has been made with the 1.2 version. OOMMF scales quite well up to 4 cores in the xeon nodes, where best results are obtained..

Node type xeon20 xeon12 xeon8
Time
776
 905 1224

More information

OOMMF home page.

OOMMF documentation.

Matlab

Maths @en, Scientific Software

General information

Version 7.9 (2009b) in the opteron nodes and 7.12 (2010a) in the Xeon nodes. Mathematical program that includes  high-level technical computing language and interactive environment for algorithm development, data visualization, data analysis, and numeric computation.

How to use

Intereactively (with graphical interface):

Matlab is only available for Opteron and Xeon so have to be used interactively from Guinness or Maiz. The graphical interface can be executed with:

matlab

In the queue system

Add the following line in the Torque scripts

/software/bin/matlab < input_file > output_file

where input_file is the file with the matlab commands and output_file is the standar output file name.

With old versions we have had problems with .m files with more than 169 lines. If this happens call your .m program from another small .m program.

To submit the calculation to the nodes add the xeon or the opteron label to submit the calculation to these kink of nodes. In addition, we only have licences to use 2 nodes, so we have the “matlab” special queue to manage them. You must use it. Therefore, your script must contain

#PBS -q matlab
#PBS -l nodes=1:ppn=1:xeon

or for the opteron nodes:

#PBS -q matlab
#PBS -l nodes=1:ppn=1:opteron

Benchmarks

Some [intlink id=”606″ type=”post”]benchmarks[/intlink] have been realized comparing [intlink id=”612″ type=”post”]Octave[/intlink], [intlink id=”606″ type=”post”]Scilab[/intlink] y Matlab.

Toolboxes

Ezyfit tool box is installed.

Optimization tool box is installed.

Statistics tool box is installed.

More information

Matlab home page.

Online documentation.

How to send Gaussian

Uncategorized @en

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. [intlink id=”237″ type=”post” target=”_blank”]Examples[/intlink].

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

Development software

Compilers and installed versions in the different architectures.

Compilers

 Xeon
 Itanium Opteron
 Pendulo
GNU ok ok ok ok
[intlink id=”454″ type=”post”]Intel[/intlink] ok ok ok ok
[intlink id=”3664″ type=”post”]Portlan (PGI)[/intlink] 10.9 10.9
[intlink id=”3672″ type=”post”]Cuda[/intlink] 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)
[intlink id=”5454″ type=”post”]HMPP[/intlink] ok

MPI

 Xeon
 Itanium
 Opteron Pendulo
[intlink id=”459″ type=”post”]HP-MPI[/intlink] ok ok
[intlink id=”459″ type=”post”]Bull-MPI[/intlink] ok ok
[intlink id=”459″ type=”post”]Intel MPI[/intlink] ok ok ok
[intlink id=”459″ type=”post”]Openmpi [/intlink] ok ok
[intlink id=”459″ type=”post”]mvapich2 1.4.1 [/intlink] ok

Libraries

 Xeon Itanium
 Opteron Pendulo
[intlink id=”447″ type=”post”]Intel MKL[/intlink] ok ok ok ok
[intlink id=”462″ type=”post”] FFTW[/intlink] ok ok ok ok
[intlink id=”3775″ type=”post”] GSL[/intlink] ok ok ok ok

ADF

Quantum Mechanics @en, Scientific Software

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

Biochemistry, MM/MD @en, Scientific Software

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.  [intlink id=”244″ type=”post”] More information about this options[/intlink]

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 @en, Scientific Software

Quantum Mechanics

 Katramila
(xeon,rh7,xeon20)		 Guinness
(xeon,oxeon)		 Kalk2017
(xeon,rh7,xeon28)
[intlink id=”573″ type=”post”]Abinit[/intlink] ok ok
[intlink id=”1591″ type=”post”]ADF[/intlink] 2017.110 2017.110 2017.110
[intlink id=”1673″ type=”post”]BigDFT[/intlink] ok ok
[intlink id=”1951″ type=”post”]Casino 2.4[/intlink] ok
[intlink id=”1543″ type=”post”]Dirac 08[/intlink] ok
[intlink id=”4807″ type=”post”]Espresso[/intlink] ok ok
[intlink id=”1563″ type=”post”]Gamess Jan 2009 [/intlink] ok
[intlink id=”12″ type=”post”]Gaussian 03 & 09[/intlink] ok ok ok
[intlink id=”467″ type=”post”]Jaguar[/intlink] ok ok ok
[intlink id=”1889″ type=”post”]MIKA .81[/intlink] ok
[intlink id=”2077″ type=”post”]NBO 5[/intlink] ok
[intlink id=”100″ type=”post”]NWChem 6.3 [/intlink] ok ok
[intlink id=”4228″ type=”post”]Orca 3.03 [/intlink]  ok ok
[intlink id=”8846″ type=”post”]PSI4[/intlink] ok ok
[intlink id=”2111″ type=”post”]Qbox[/intlink] ok ok
[intlink id=”2085″ type=”post”]Qsite[/intlink]  ok ok ok
[intlink id=”7190″ type=”post”]Siesta 2.0.1[/intlink] ok
[intlink id=”7190″ type=”post”]Siesta 3.0[/intlink] ok
[intlink id=”39″ type=”post”]TB-LMTO 4.6 [/intlink] ok
[intlink id=”3889″ type=”post”]Terachem [/intlink] ok
[intlink id=”4705″ type=”post”]Turbomole 7.0 [/intlink]  ok ok
[intlink id=”98″ type=”post”]VASP[/intlink] ok ok ok
[intlink id=”1637″ type=”post”]Wien2K[/intlink] ok ok
[intlink id=”1655″ type=”post”]Yambo 3.2.2 [/intlink] ok ok

BioChemistry / Molecular Mechanics

 Katramila
(xeon,rh7,xeon20)		 Guinness
(xeon,oxeon)		 Kalk2017
(xeon,rh7,xeon28)
[intlink id=”8263″ type=”post”]Amber[/intlink] ok ok
[intlink id=”4883″ type=”post”]DL_POLY [/intlink] ok ok
[intlink id=”1989″ type=”post”]Gromacs[/intlink] ok ok
[intlink id=”5739″ type=”post”] Gulp 4.0 [/intlink] ok
[intlink id=”5683″ type=”post”]LAMMPS [/intlink] ok
[intlink id=”2065″ type=”post”]Macromodel[/intlink] ok ok ok
[intlink id=”2011″ type=”post”]NAMD 2.6 [/intlink] ok
[intlink id=”5809″ type=”post”] Towhee 7.0.2  [/intlink] ok

Mathematics

 Katramila
(xeon,rh7,xeon20)		 Guinness
(xeon,oxeon)		 Kalk2017
(xeon,rh7,xeon28)
[intlink id=”5224″ type=”post”] Coin-or [/intlink] ok ok
[intlink id=”5240″ type=”post”] CPLEX [/intlink] ok ok
[intlink id=”1363″ type=”post”]Grace 5.1.19 [/intlink] ok ok
[intlink id=”598″ type=”post”]Mathematica [/intlink]  8.0 ok ok
[intlink id=”4255″ type=”post”]Matlab[/intlink] ok ok
[intlink id=”1371″ type=”post”]Matplotlib[/intlink] ok
[intlink id=”612″ type=”post”]Octave 3.2.3 [/intlink] ok
[intlink id=”612″ type=”post”]Octave 3.2.4 [/intlink] ok
[intlink id=”8635″ type=”post”]R, RCommander and RStudio[/intlink] 3.3.3 3.3.2 2.7.0
[intlink id=”606″ type=”post”]Scilab 5.1.1 [/intlink] ok
[intlink id=”606″ type=”post”]Scilab 5.2.2 [/intlink] ok

Genetics

 Katramila
(xeon,rh7,xeon20)		 Guinness
(xeon,oxeon)		 Kalk2017
(xeon,rh7,xeon28)
[intlink id=”6200″ type=”post”]ABySS[/intlink] ok
[intlink id=”1477″ type=”post”]BEAST[/intlink] ok ok
[intlink id=”6021″ type=”post”]BLAST [/intlink] ok
[intlink id=”1493″ type=”post”]Blast2Go [/intlink] ok
[intlink id=”6131″ type=”post”]Clean_reads[/intlink] ok
[intlink id=”5893″ type=”post”]CLUMPP[/intlink] ok
[intlink id=”7668″ type=”post”] Cufflinks [/intlink] ok
[intlink id=”5927″ type=”post”]Genepop[/intlink] ok
[intlink id=”8059″ type=”post”]IDBA-UD[/intlink] ok ok
[intlink id=”7981″ type=”post”]MetAMOS[/intlink] ok
[intlink id=”1495″ type=”post”]mpiBLAST [/intlink] ok
[intlink id=”7758″ type=”post”]QIIME[/intlink] ok
[intlink id=”8023″ type=”post”]SPAdes[/intlink] ok ok
[intlink id=”5875″ type=”post”]Structure [/intlink] ok
[intlink id=”7660″ type=”post”]TopHat [/intlink] ok
[intlink id=”7105″ type=”post”]Trinity[/intlink] ok
[intlink id=”7744″ type=”post”]USEARCH[/intlink] ok
[intlink id=”6043″ type=”post”]Velvet[/intlink] ok

Visualization

 Katramila
(xeon,rh7,xeon20)		 Guinness
(xeon,oxeon)		 Kalk2017
(xeon,rh7,xeon28)
[intlink id=”5366″ type=”post”]Gaussview[/intlink] ok
[intlink id=”4012″ type=”post”] Maestro [/intlink] ok ok
[intlink id=”1275″ type=”post”] Molden[/intlink] ok ok ok
[intlink id=”1229″ type=”post”]NX client[/intlink] ok
[intlink id=”1353″ type=”post”] P4VASP [/intlink] ok
x2Go ok ok
[intlink id=”5544″ type=”post”] XCrysDen [/intlink] ok
[intlink id=”1261″ type=”post”] Xmakemol [/intlink]  ok ok
[intlink id=”3550″ type=”post”] VMD [/intlink] ok ok

Other Software

 Katramila
(xeon,rh7,xeon20)		 Guinness
(xeon,oxeon)		 Kalk2017
(xeon,rh7,xeon28)
[intlink id=”1389″ type=”post”] GAP 4.4 [/intlink] ok
[intlink id=”5483″ type=”post”] Gretl [/intlink] ok
[intlink id=”1379″ type=”post”] HTK 3.4.1 [/intlink]
[intlink id=”1871″ type=”post”] NCL-NCAR [/intlink] ok
[intlink id=”1581″ type=”post”] OOMMF [/intlink]  ok ok
[intlink id=”6882″ type=”post”] PHENIX[/intlink] ok
[intlink id=”8520″ type=”post”] SCIPION[/intlink] ok
[intlink id=”576″ type=”post”] STAR-CCM+[/intlink] ok ok ok
[intlink id=”1875″ type=”post”] WRF 3.1 [/intlink] ok

 

Maestro

Scientific Software, Visualization

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 [intlink id=”48″ type=”post”]access guide[/intlink] of the service.

To execute Maestro run in the terminal

maestro

More information

Maestro web page.

Schrödinger web page.

Terachem

Quantum Mechanics @en, Scientific Software

General information

TeraChem 1.45 is general purpose quantum chemistry software designed to run on NVIDIA GPU architectures under a 64-bit Linux operating system. Some of TeraChem features include:

  • Full support for both NVIDIA Tesla and Fermi GPUs
  • Restricted Hartree-Fock and Kohn-Sham single point energy and gradient calculations
  • Various DFT functionals (BLYP, B3LYP, PBE, etc) and DFT grids (800-80,000 grid points per atom)
  • Empirical dispersion corrections (DFT-D)
  • Geometry optimization and transition state search (including constraints)
  • Ab initio molecular dynamics (NVE and NVT ensembles)
  • Support of multiple-GPU systems
  • Up to 1000 times faster than conventional CPU-based codes
  • Designed for large molecules – reads/writes PDB files directly
  • Optimization including geometric constraints
  • Improved mixed-precision for increased accuracy

How to send Terachem

[intlink id=”3851″ type=”post”]send_terachem[/intlink] command exist to facilitate the job submision to the cluster.

More information

Terachem web page.

User guide.