SNIC Documentation - User contributions [en]

Rosetta

2015-12-02T17:15:09Z

Åke Sandgren (HPC2N): /* License */

{{software info
|description=protein structure prediction suite
|license=site license
|fields=Bioinformatics
}}
[http://www.rosettacommons.org/ {{PAGENAME}}] is a {{#show: {{PAGENAME}} |?description}} that can also be used for structure design and to investigate protein-protein interactions.

== Availability ==
{{list resources for software}}

== Compilation and installation ==
Rosetta 3.4 does not seem to compile with Intel 12 compilers, though it is possible to use Intel 11 compilers by explicitly setting the compiler path in rosetta_source/tools/build/user.settings and then building with the cxx=icc option to scons. Rosetta does not seem to support setting an install prefix at build time, but assumes that the source files will be copied to the install location and built in-place, but this isn't actually needed, as you can copy executables and libraries to any directory after the build completes. Note however that Rosetta rpaths its own shared libraries inside the build tree, so removing the build tree will break the program if you don't change the rpaths, using for example chrpath.

Rosetta also likes to name its executables after the operating system, compiler and mode of compilation, and also indicates "default" builds using name mangling (e.g: vip.default.linuxiccrelease). This is purely cosmetic and can be changed (e.g. to just vip). It is however worth bearing in mind that some third-party applications (like [[CS-Rosetta]]) will make assumptions on your build choices and only look for executables named *.linuxgccrelease (note not default), and their configurations will thus have to be modified accordingly.

Rosetta also needs a database directory tree, which you can point out using the $ROSETTA3_DB environment variable so that users do not have to use the -database option at each launch of a Rosetta executable.

== License ==
{{show license}}

[[NSC]] has a site license for academic users.

[[HPC2N]] has a site license for academic users.

== Experts ==
{{list experts}}

== Links ==
* [http://www.rosettacommons.org/ Official website]

Rosetta

2015-12-02T17:14:49Z

Åke Sandgren (HPC2N):

{{software info
|description=protein structure prediction suite
|license=site license
|fields=Bioinformatics
}}
[http://www.rosettacommons.org/ {{PAGENAME}}] is a {{#show: {{PAGENAME}} |?description}} that can also be used for structure design and to investigate protein-protein interactions.

== Availability ==
{{list resources for software}}

== Compilation and installation ==
Rosetta 3.4 does not seem to compile with Intel 12 compilers, though it is possible to use Intel 11 compilers by explicitly setting the compiler path in rosetta_source/tools/build/user.settings and then building with the cxx=icc option to scons. Rosetta does not seem to support setting an install prefix at build time, but assumes that the source files will be copied to the install location and built in-place, but this isn't actually needed, as you can copy executables and libraries to any directory after the build completes. Note however that Rosetta rpaths its own shared libraries inside the build tree, so removing the build tree will break the program if you don't change the rpaths, using for example chrpath.

Rosetta also likes to name its executables after the operating system, compiler and mode of compilation, and also indicates "default" builds using name mangling (e.g: vip.default.linuxiccrelease). This is purely cosmetic and can be changed (e.g. to just vip). It is however worth bearing in mind that some third-party applications (like [[CS-Rosetta]]) will make assumptions on your build choices and only look for executables named *.linuxgccrelease (note not default), and their configurations will thus have to be modified accordingly.

Rosetta also needs a database directory tree, which you can point out using the $ROSETTA3_DB environment variable so that users do not have to use the -database option at each launch of a Rosetta executable.

== License ==
{{show license}}

[[NSC]] has a site license for academic users.
[[HPC2N]] has a site license for academic users.

== Experts ==
{{list experts}}

== Links ==
* [http://www.rosettacommons.org/ Official website]

User:Åke Sandgren (HPC2N)

2013-03-21T11:44:42Z

Åke Sandgren (HPC2N):

{{application expert info
|first name=Åke
|last name=Sandgren
|centre=HPC2N
|fields=Computational science
|fte=50
|snic ae financing=50
|other ae financing=
|financing=SNIC
|general activities=SGUSI
|other activities=


}}

== Quick facts ==
* Working at HPC2N since 1997
* Working on debugging, benchmarking, optimization and scaling issues
* Involved in PRACE

== Expertise ==
* [[expertise::Fortran]]

User:Åke Sandgren (HPC2N)

2013-03-21T11:42:28Z

Åke Sandgren (HPC2N):

{{application expert info
|first name=Åke
|last name=Sandgren
|centre=HPC2N
|fields=Computational science
|fte=50
|snic ae financing=50
|other ae financing=
|financing=SNIC
|general activities=SGUSI
|other activities=


}}

Abisko

2013-03-21T11:36:24Z

Åke Sandgren (HPC2N):

{{resource info
|description=capability resource of 153 TFLOPS with full bisectional infiniband interconnect
|resource type=compute
|centre=HPC2N
|production=yes
|commissioning date=November 2011
|decommissioning date=
|software=GROMACS, Gnuplot, Nwchem, openfoam, Quantum Espresso, SIESTA, TURBOMOLE, VASP, ABINIT, acml, ansys, gaussian, hdf5, matlab, NAMD, ASE, intel compiler suite, PGI, PathScale, Open MPI, ARC client, GPAW, CP2K, Amber, Code_Saturne, DDT, GAMESS, FFTW, SciPy, NumPy,
MKL, Rosetta, VMD, Trace analyzer and collector, VTune Amplifier, R, Octave, Molpro, Intel MPI, Inspector
}}

== Available software ==
{{list software at resource}}

== Links ==
* [http://www.hpc2n.umu.se/resources/abisko System details]

Abisko

2013-03-21T11:36:04Z

Åke Sandgren (HPC2N):

{{resource info
|description=capability resource of 153 TFLOPS with full bisectional infiniband interconnect
|resource type=compute
|centre=HPC2N
|production=yes
|commissioning date=November 2011
|decommissioning date=
|software=GROMACS, Gnuplot, Nwchem, openfoam, Quantum Espresso, SIESTA, TURBOMOLE, VASP, ABINIT, acml, ansys, gaussian, hdf5, matlab, NAMD, ASE, intel compiler suite, PGI, PathScale, Open MPI, ARC client, GPAW, CP2K, Amber, Code_Saturne, DDT, GAMESS, FFTW, SciPy, NumPy,
MKL, Rosetta, VMD, Trace analyzer and collector, VTune Amplifier, R, Octave, Molpro, Intel MPI
}}

== Available software ==
{{list software at resource}}

== Links ==
* [http://www.hpc2n.umu.se/resources/abisko System details]

Abisko

2013-03-21T11:35:28Z

Åke Sandgren (HPC2N):

{{resource info
|description=capability resource of 153 TFLOPS with full bisectional infiniband interconnect
|resource type=compute
|centre=HPC2N
|production=yes
|commissioning date=November 2011
|decommissioning date=
|software=GROMACS, Gnuplot, Nwchem, openfoam, Quantum Espresso, SIESTA, TURBOMOLE, VASP, ABINIT, acml, ansys, gaussian, hdf5, matlab, NAMD, ASE, intel compiler suite, PGI, PathScale, Open MPI, ARC client, GPAW, CP2K, Amber, Code_Saturne, DDT, GAMESS, FFTW, SciPy, NumPy,
MKL, Rosetta, VMD, Trace analyzer and collector, VTune Amplifier, R, Octave, Molpro
}}

== Available software ==
{{list software at resource}}

== Links ==
* [http://www.hpc2n.umu.se/resources/abisko System details]

Abisko

2013-03-21T11:33:51Z

Åke Sandgren (HPC2N):

{{resource info
|description=capability resource of 153 TFLOPS with full bisectional infiniband interconnect
|resource type=compute
|centre=HPC2N
|production=yes
|commissioning date=November 2011
|decommissioning date=
|software=GROMACS, Gnuplot, Nwchem, openfoam, Quantum Espresso, SIESTA, TURBOMOLE, VASP, ABINIT, acml, ansys, gaussian, hdf5, matlab, NAMD, ASE, intel compiler suite, PGI, PathScale, Open MPI, ARC client, GPAW, CP2K, Amber, Code_Saturne, DDT, GAMESS, FFTW, SciPy, NumPy,
MKL, Rosetta, VMD, Trace analyzer and collector, VTune Amplifier, R, Octave
}}

== Available software ==
{{list software at resource}}

== Links ==
* [http://www.hpc2n.umu.se/resources/abisko System details]

PathScale

2013-03-21T11:32:12Z

Åke Sandgren (HPC2N): Created page with "{{software info |description=compiler suite |license=site license |fields=System tool }} [http://www.pathscale.com/ {{PAGENAME}}] (PathScale Inc) is a {{#show: {{PAGENAME}} |?des..."

{{software info
|description=compiler suite
|license=site license
|fields=System tool
}}
[http://www.pathscale.com/ {{PAGENAME}}] (PathScale Inc) is a {{#show: {{PAGENAME}} |?description}} for C, C++ and Fortran.

== Availability ==
{{list resources for software}}


== License ==
{{show license}}

[[HPC2N]] has a site licenses.

== Experts ==
{{list experts}}

== Links ==
* [http://www.pathscale.com/ Official website]

Abisko

2013-03-21T11:28:22Z

Åke Sandgren (HPC2N):

{{resource info
|description=capability resource of 153 TFLOPS with full bisectional infiniband interconnect
|resource type=compute
|centre=HPC2N
|production=yes
|commissioning date=November 2011
|decommissioning date=
|software=GROMACS, Gnuplot, Nwchem, openfoam, Quantum Espresso, SIESTA, TURBOMOLE, VASP, ABINIT, acml, ansys, gaussian, hdf5, matlab, NAMD, ASE, intel compiler suite, PGI, PathScale, Open MPI, ARC client, GPAW, CP2K, Amber, Code_Saturne, DDT, GAMESS, FFTW, SciPy, NumPy,
MKL, Rosetta, VMD, Trace analyzer and collector, VTune Amplifier, R
}}

== Available software ==
{{list software at resource}}

== Links ==
* [http://www.hpc2n.umu.se/resources/abisko System details]

Abisko

2013-03-21T11:27:50Z

Åke Sandgren (HPC2N):

{{resource info
|description=capability resource of 153 TFLOPS with full bisectional infiniband interconnect
|resource type=compute
|centre=HPC2N
|production=yes
|commissioning date=November 2011
|decommissioning date=
|software=GROMACS, Gnuplot, Nwchem, openfoam, Quantum Espresso, SIESTA, TURBOMOLE, VASP, ABINIT, acml, ansys, gaussian, hdf5, matlab, NAMD, ASE, intel compiler suite, PGI, PathScale, Open MPI, ARC client, GPAW, CP2K, Amber, Code_Saturne, DDT, GAMESS, FFTW, SciPy, NumPy,
MKL, Rosetta, VMD, Trace analyzer and collector, VTune Amplifier
}}

== Available software ==
{{list software at resource}}

== Links ==
* [http://www.hpc2n.umu.se/resources/abisko System details]

Abisko

2013-03-21T10:37:58Z

Åke Sandgren (HPC2N):

{{resource info
|description=capability resource of 153 TFLOPS with full bisectional infiniband interconnect
|resource type=compute
|centre=HPC2N
|production=yes
|commissioning date=November 2011
|decommissioning date=
|software=GROMACS, Gnuplot, Nwchem, openfoam, Quantum Espresso, SIESTA, TURBOMOLE, VASP, ABINIT, acml, ansys, gaussian, hdf5, matlab, NAMD, ASE, intel compiler suite, PGI, PathScale, Open MPI, ARC client, GPAW, CP2K, Amber, Code_Saturne, DDT, GAMESS, FFTW, SciPy, NumPy,
MKL, Rosetta
}}

== Available software ==
{{list software at resource}}

== Links ==
* [http://www.hpc2n.umu.se/resources/abisko System details]

Abisko

2013-03-21T10:35:14Z

Åke Sandgren (HPC2N):

{{resource info
|description=capability resource of 153 TFLOPS with full bisectional infiniband interconnect
|resource type=compute
|centre=HPC2N
|production=yes
|commissioning date=November 2011
|decommissioning date=
|software=GROMACS, Gnuplot, Nwchem, openfoam, Quantum Espresso, SIESTA, TURBOMOLE, VASP, ABINIT, acml, ansys, gaussian, hdf5, matlab, NAMD, ASE, intel compiler suite, PGI, PathScale, Open MPI, ARC client, GPAW, CP2K, Amber, Code_Saturne, DDT, GAMESS, FFTW, SciPy, NumPy,
MKL
}}

== Available software ==
{{list software at resource}}

== Links ==
* [http://www.hpc2n.umu.se/resources/abisko System details]

Abisko

2013-03-21T10:34:36Z

Åke Sandgren (HPC2N):

{{resource info
|description=capability resource of 153 TFLOPS with full bisectional infiniband interconnect
|resource type=compute
|centre=HPC2N
|production=yes
|commissioning date=November 2011
|decommissioning date=
|software=GROMACS, Gnuplot, Nwchem, openfoam, Quantum Espresso, SIESTA, TURBOMOLE, VASP, ABINIT, acml, ansys, gaussian, hdf5, matlab, NAMD, ASE, intel compiler suite, PGI, PathScale, Open MPI, ARC client, GPAW, CP2K, Amber, Code_Saturne, DDT, GAMESS, FFTW, SciPy, NumPy
}}

== Available software ==
{{list software at resource}}

== Links ==
* [http://www.hpc2n.umu.se/resources/abisko System details]

Abisko

2013-03-21T10:33:39Z

Åke Sandgren (HPC2N):

{{resource info
|description=capability resource of 153 TFLOPS with full bisectional infiniband interconnect
|resource type=compute
|centre=HPC2N
|production=yes
|commissioning date=November 2011
|decommissioning date=
|software=GROMACS, Gnuplot, Nwchem, openfoam, Quantum Espresso, SIESTA, TURBOMOLE, VASP, ABINIT, acml, ansys, gaussian, hdf5, matlab, NAMD, ASE, intel compiler suite, PGI, PathScale, Open MPI, ARC client, GPAW, CP2K, Amber, Code_Saturne, DDT, GAMESS, FFTW
}}

== Available software ==
{{list software at resource}}

== Links ==
* [http://www.hpc2n.umu.se/resources/abisko System details]

Abisko

2013-03-21T10:32:42Z

Åke Sandgren (HPC2N):

{{resource info
|description=capability resource of 153 TFLOPS with full bisectional infiniband interconnect
|resource type=compute
|centre=HPC2N
|production=yes
|commissioning date=November 2011
|decommissioning date=
|software=GROMACS, Gnuplot, Nwchem, openfoam, Quantum Espresso, SIESTA, TURBOMOLE, VASP, ABINIT, acml, ansys, gaussian, hdf5, matlab, NAMD, ASE, intel compiler suite, PGI, PathScale, Open MPI, ARC client, GPAW, CP2K, Amber, Code_Saturne, DDT, GAMESS
}}

== Available software ==
{{list software at resource}}

== Links ==
* [http://www.hpc2n.umu.se/resources/abisko System details]

Abisko

2013-03-21T10:30:11Z

Åke Sandgren (HPC2N):

{{resource info
|description=capability resource of 153 TFLOPS with full bisectional infiniband interconnect
|resource type=compute
|centre=HPC2N
|production=yes
|commissioning date=November 2011
|decommissioning date=
|software=GROMACS, Gnuplot, Nwchem, openfoam, Quantum Espresso, SIESTA, TURBOMOLE, VASP, ABINIT, acml, ansys, gaussian, hdf5, matlab, NAMD, ASE, intel compiler suite, PGI, PathScale, Open MPI, ARC client, GPAW, CP2K, Amber, Code_Saturne, DDT
}}

== Available software ==
{{list software at resource}}

== Links ==
* [http://www.hpc2n.umu.se/resources/abisko System details]

Abisko

2013-03-21T10:29:42Z

Åke Sandgren (HPC2N):

{{resource info
|description=capability resource of 153 TFLOPS with full bisectional infiniband interconnect
|resource type=compute
|centre=HPC2N
|production=yes
|commissioning date=November 2011
|decommissioning date=
|software=GROMACS, Gnuplot, Nwchem, openfoam, Quantum Espresso, SIESTA, TURBOMOLE, VASP, ABINIT, acml, ansys, gaussian, hdf5, matlab, NAMD, ASE, intel compiler suite, PGI, PathScale, Open MPI, ARC client, GPAW, CP2K, Amber, Code_Saturne
}}

== Available software ==
{{list software at resource}}

== Links ==
* [http://www.hpc2n.umu.se/resources/abisko System details]

Abisko

2013-03-21T10:27:19Z

Åke Sandgren (HPC2N):

{{resource info
|description=capability resource of 153 TFLOPS with full bisectional infiniband interconnect
|resource type=compute
|centre=HPC2N
|production=yes
|commissioning date=November 2011
|decommissioning date=
|software=GROMACS, Gnuplot, Nwchem, openfoam, Quantum Espresso, SIESTA, TURBOMOLE, VASP, ABINIT, acml, ansys, gaussian, hdf5, matlab, NAMD, ASE, intel compiler suite, PGI, PathScale, Open MPI, ARC client, GPAW, CP2K, Amber
}}

== Available software ==
{{list software at resource}}

== Links ==
* [http://www.hpc2n.umu.se/resources/abisko System details]

Abisko

2013-03-21T10:26:35Z

Åke Sandgren (HPC2N):

{{resource info
|description=capability resource of 153 TFLOPS with full bisectional infiniband interconnect
|resource type=compute
|centre=HPC2N
|production=yes
|commissioning date=November 2011
|decommissioning date=
|software=GROMACS, Gnuplot, Nwchem, openfoam, Quantum Espresso, SIESTA, TURBOMOLE, VASP, ABINIT, acml, ansys, gaussian, hdf5, matlab, NAMD, ASE, intel compiler suite, PGI, PathScale, Open MPI, ARC client, GPAW, CP2K
}}

== Available software ==
{{list software at resource}}

== Links ==
* [http://www.hpc2n.umu.se/resources/abisko System details]

Abisko

2013-03-21T10:26:07Z

Åke Sandgren (HPC2N):

{{resource info
|description=capability resource of 153 TFLOPS with full bisectional infiniband interconnect
|resource type=compute
|centre=HPC2N
|production=yes
|commissioning date=November 2011
|decommissioning date=
|software=GROMACS, Gnuplot, Nwchem, openfoam, Quantum Espresso, SIESTA, TURBOMOLE, VASP, ABINIT, acml, ansys, gaussian, hdf5, matlab, NAMD, ASE, intel compiler suite, PGI, PathScale, Open MPI, ARC client, GPAW
}}

== Available software ==
{{list software at resource}}

== Links ==
* [http://www.hpc2n.umu.se/resources/abisko System details]

Akka

2012-06-20T19:18:47Z

Åke Sandgren (HPC2N):

{{resource info
|description=capability cluster resource of 54 TFLOPS with infiniband interconnect
|centre=HPC2N
|production=yes
|commissioning date=August 2008
|decommissioning date=
|software=ABINIT, Amber, ARC client, ASE, Charmm, CP2K, Dacapo, Desmond, Edge, ESPResSo, GAMESS, Gamess-UK, Gaussian, Gnuplot, GPAW, Grace, GROMACS, HMMER, Intel MPI, Intel compiler suite, Jaguar, Matlab, MKL, Molden, MPQC, NumPy, Octave, OpenFOAM, Open MPI, PathScale, PGI, Quantum Espresso, R, SIESTA, Trace analyzer and collector, VASP, vmd, vtune amplifier, WRF
}}

== Available software ==
{{list software at resource}}

== Links ==
* [http://www.hpc2n.umu.se/resources/akka/ System details]

User:Åke Sandgren (HPC2N)

2012-04-02T13:24:15Z

Åke Sandgren (HPC2N):

{{application expert info
|first name=Åke
|last name=Sandgren
|centre=HPC2N
|fields=Computational science
|fte=50
|snic ae financing=50
|other ae financing=
|financing=SNIC
|general activities=SGUSI
|other activities=


}}

Abisko

2012-03-15T08:44:47Z

Åke Sandgren (HPC2N):

{{resource info
|description=capability resource of 153 TFLOPS with full bisectional infiniband interconnect
|centre=HPC2N
|production=yes
|commissioning date=November 2011
|decommissioning date=
|software=GROMACS, Gnuplot, Nwchem, openfoam, Quantum Espresso, SIESTA, TURBOMOLE, VASP, ABINIT, acml, ansys, gaussian, hdf5, matlab, NAMD, ASE, intel compiler suite, PGI, PathScale, Open MPI, ARC client
}}

== Available software ==
{{list software at resource}}

== Links ==
* [http://www.hpc2n.umu.se/resources/abisko System details]

Abisko

2012-03-15T08:40:26Z

Åke Sandgren (HPC2N):

{{resource info
|description=capability resource of 153 TFLOPS with full bisectional infiniband interconnect
|centre=HPC2N
|production=yes
|commissioning date=November 2011
|decommissioning date=
|software=GROMACS, Gnuplot, Nwchem, openfoam, Quantum Espresso, SIESTA, TURBOMOLE, VASP, ABINIT, acml, ansys, gaussian, hdf5, matlab, NAMD, ASE, intel compiler suite, PGI, PathScale, Open MPI
}}

== Available software ==
{{list software at resource}}

== Links ==
* [http://www.hpc2n.umu.se/resources/abisko System details]

Akka

2012-03-15T08:40:07Z

Åke Sandgren (HPC2N):

{{resource info
|description=capability cluster resource of 54 TFLOPS with infiniband interconnect
|centre=HPC2N
|production=yes
|commissioning date=August 2008
|decommissioning date=
|software=ABINIT, Amber, ARC client, ASE, Charmm, CP2K, Dacapo, Desmond, Edge, ESPResSo, GAMESS, Gamess-UK, Gaussian, Gnuplot, GPAW, Grace, GROMACS, HMMER, Intel MPI, Intel compiler suite, Matlab, MKL, Molden, MPQC, NumPy, Octave, OpenFOAM, Open MPI, PathScale, PGI, Quantum Espresso, R, SIESTA, Trace analyzer and collector, VASP, vmd, vtune amplifier, WRF
}}

== Available software ==
{{list software at resource}}

== Links ==
* [http://www.hpc2n.umu.se/resources/akka/ System details]

Abisko

2012-03-15T08:39:09Z

Åke Sandgren (HPC2N):

{{resource info
|description=capability resource of 153 TFLOPS with full bisectional infiniband interconnect
|centre=HPC2N
|production=yes
|commissioning date=November 2011
|decomissioning date=
|software=GROMACS, Gnuplot, Nwchem, openfoam, Quantum Espresso, SIESTA, TURBOMOLE, VASP, ABINIT, acml, ansys, gaussian, hdf5, matlab, NAMD, ASE, intel compiler suite, PGI, PathScale, Open MPI
}}

== Available software ==
{{list software at resource}}

== Links ==
* [http://www.hpc2n.umu.se/resources/abisko System details]

Abisko

2012-02-24T16:17:35Z

Åke Sandgren (HPC2N):

{{resource info
|description=capability resource of 153 TFLOPS with full bisectional infiniband interconnect
|centre=HPC2N
|software=GROMACS, Gnuplot, Nwchem, openfoam, Quantum Espresso, SIESTA, TURBOMOLE, VASP, ABINIT, acml, ansys, gaussian, hdf5, matlab, NAMD, ASE, intel compiler suite, PGI, PathScale, Open MPI
}}

== Available software ==
{{list software at resource}}

== Links ==
* [http://www.hpc2n.umu.se/resources/abisko System details]

Abisko

2012-02-24T16:17:03Z

Åke Sandgren (HPC2N):

{{resource info
|description=capability resource of 153 TFLOPS with full bisectional infiniband interconnect
|centre=HPC2N
|software=GROMACS, Gnuplot, Nwchem, openfoam, Quantum Espresso, SIESTA, TURBOMOLE, VASP, ABINIT, acml, ansys, gaussian, hdf5, matlab, NAMD, ASE, intel compiler suite, PGI, PathScale
}}

== Available software ==
{{list software at resource}}

== Links ==
* [http://www.hpc2n.umu.se/resources/abisko System details]

Akka

2012-02-24T16:14:44Z

Åke Sandgren (HPC2N):

{{resource info
|description=capability cluster resource of 54 TFLOPS with infiniband interconnect
|centre=HPC2N
|software=ABINIT, Amber, ARC client, ASE, Charmm, CP2K, Dacapo, Desmond, Edge, ESPResSo, GAMESS, Gamess-UK, Gaussian, Gnuplot, GPAW, Grace, GROMACS, HMMER, Intel MPI, Intel compiler suite, Matlab, MKL, Molden, MPQC, NumPy, Octave, OpenFOAM, Open MPI, PathScale, PGI, Quantum Espresso, R, SIESTA, Trace analyzer and collector, VASP, vmd, vtune amplifier, WRF
}}

== Available software ==
{{list software at resource}}

== Links ==
* [http://www.hpc2n.umu.se/resources/akka/ System details]

Akka

2012-02-24T16:13:31Z

Åke Sandgren (HPC2N):

{{resource info
|description=capability cluster resource of 54 TFLOPS with infiniband interconnect
|centre=HPC2N
|software=ABINIT, Amber, ARC client, ASE, Charmm, CP2K, Dacapo, Desmond, Edge, ESPResSo, Gamess-UK, Gaussian, Gnuplot, GPAW, Grace, GROMACS, HMMER, Intel MPI, Intel compiler suite, Matlab, MKL, Molden, MPQC, NumPy, Octave, OpenFOAM, Open MPI, PathScale, PGI, Quantum Espresso, R, SIESTA, Trace analyzer and collector, VASP, vmd, vtune amplifier, WRF
}}

== Available software ==
{{list software at resource}}

== Links ==
* [http://www.hpc2n.umu.se/resources/akka/ System details]

Akka

2012-02-24T16:13:15Z

Åke Sandgren (HPC2N):

{{resource info
|description=capability cluster resource of 54 TFLOPS with infiniband interconnect
|centre=HPC2N
|software=ABINIT, Amber, ARC Client, ASE, Charmm, CP2K, Dacapo, Desmond, Edge, ESPResSo, Gamess-UK, Gaussian, Gnuplot, GPAW, Grace, GROMACS, HMMER, Intel MPI, Intel compiler suite, Matlab, MKL, Molden, MPQC, NumPy, Octave, OpenFOAM, Open MPI, PathScale, PGI, Quantum Espresso, R, SIESTA, Trace analyzer and collector, VASP, vmd, vtune amplifier, WRF
}}

== Available software ==
{{list software at resource}}

== Links ==
* [http://www.hpc2n.umu.se/resources/akka/ System details]

Abisko

2012-02-24T16:11:48Z

Åke Sandgren (HPC2N):

{{resource info
|description=capability resource of 153 TFLOPS with full bisectional infiniband interconnect
|centre=HPC2N
|software=GROMACS, Gnuplot, Nwchem, openfoam, Quantum Espresso, SIESTA, TURBOMOLE, VASP, ABINIT, acml, ansys, gaussian, hdf5, matlab, NAMD, ASE, intel compiler suite, PGI, PSC
}}

== Available software ==
{{list software at resource}}

== Links ==
* [http://www.hpc2n.umu.se/resources/abisko System details]

Abisko

2012-02-24T16:10:58Z

Åke Sandgren (HPC2N):

{{resource info
|description=capability resource of 153 TFLOPS with full bisectional infiniband interconnect
|centre=HPC2N
|software=GROMACS, Gnuplot, Nwchem, openfoam, Quantum Espresso, SIESTA, TURBOMOLE, VASP, ABINIT, acml, ansys, gaussian, hdf5, matlab, NAMD, ASE
}}

== Available software ==
{{list software at resource}}

== Links ==
* [http://www.hpc2n.umu.se/resources/abisko System details]

Abisko

2012-02-24T16:07:43Z

Åke Sandgren (HPC2N):

{{resource info
|description=capability resource of 153 TFLOPS with full bisectional infiniband interconnect
|centre=HPC2N
|software=GROMACS, Gnuplot, Nwchem, openfoam, Quantum Espresso, SIESTA, TURBOMOLE, VASP, ABINIT, acml, ansys, gaussian, hdf5, matlab, namd
}}

== Available software ==
{{list software at resource}}

== Links ==
* [http://www.hpc2n.umu.se/resources/abisko System details]

Abisko

2012-02-24T16:07:14Z

Åke Sandgren (HPC2N):

{{resource info
|description=capability resource of 153 TFLOPS with full bisectional infiniband interconnect
|centre=HPC2N
|software=GROMACS, Gnuplot, Nwchem, openfoam, Quantum Espresso, SIESTA, TURBOMOLE, VASP, abinit, acml, ansys, gaussian, hdf5, matlab, namd
}}

== Available software ==
{{list software at resource}}

== Links ==
* [http://www.hpc2n.umu.se/resources/abisko System details]

Abisko

2011-10-18T13:28:06Z

Åke Sandgren (HPC2N):

{{resource info
|description=capability resource of 153 TFLOPS with full bisectional infiniband interconnect
|centre=HPC2N
|software=GROMACS, Gnuplot, Nwchem, openfoam, Quantum Espresso, SIESTA, TURBOMOLE, VASP
}}

== Available software ==
{{list software at resource}}

== Links ==
* [http://www.hpc2n.umu.se/resources/abisko System details]

Abisko

2011-10-18T13:25:59Z

Åke Sandgren (HPC2N):

{{resource info
|description=capability resource of 153 TFLOPS with full bisectional infiniband interconnect
|centre=HPC2N
|software=GROMACS, Gnuplot, Nwchem, Quantum Espresso, SIESTA, TURBOMOLE, VASP
}}

== Available software ==
{{list software at resource}}

== Links ==
* [http://www.hpc2n.umu.se/resources/abisko System details]

Akka

2011-09-29T08:47:40Z

Åke Sandgren (HPC2N):

{{resource info
|description=capability cluster resource of 54 TFLOPS with infiniband interconnect
|centre=HPC2N
|software=ABINIT, Amber, Arc Client, ASE, Charmm, CP2K, Dacapo, Desmond, Edge, ESPResSo, Gamess-UK, Gaussian, Gnuplot, GPAW, Grace, GROMACS, HMMER, Intel MPI, Intel compiler suite, Matlab, MKL, Molden, MPQC, NumPy, Octave, OpenFOAM, Open MPI, PathScale, PGI, Quantum Espresso, R, SIESTA, Trace analyzer and collector, VASP, vmd, vtune amplifier, WRF
}}

== Available software ==
{{list software at resource}}

== Links ==
* [http://www.hpc2n.umu.se/resources/akka/ System details]

Akka

2011-09-29T07:20:54Z

Åke Sandgren (HPC2N):

{{resource info
|description=capability cluster resource of 54 TFLOPS with infiniband interconnect
|centre=HPC2N
|software=ABINIT, Amber, Charmm, CP2K, Dacapo, Desmond, Edge, ESPResSo, Gamess-UK, Gaussian, Gnuplot, GPAW, GROMACS, HMMER, Matlab, MPQC, OpenFOAM, Quantum Espresso, SIESTA, VASP, WRF
}}

== Available software ==
{{list software at resource}}

== Links ==
* [http://www.hpc2n.umu.se/resources/akka/ System details]

Abisko

2011-09-29T07:09:44Z

Åke Sandgren (HPC2N):

{{resource info
|description=capability resource of 153 TFLOPS with full bisectional infiniband interconnect
|centre=HPC2N
|software=GROMACS, Gnuplot, Nwchem, Quantum Espresso, SIESTA, VASP
}}

== Available software ==
{{list software at resource}}

== Links ==
* [http://www.hpc2n.umu.se/resources/abisko System details]

User:Åke Sandgren (HPC2N)

2011-09-29T06:54:59Z

Åke Sandgren (HPC2N):

{{application expert info
|first name=Åke
|last name=Sandgren
|centre=HPC2N
|fields=Computational science
|fte=50
|financing=SNIC
|general activities=SGUSI
|other activities=


}}

User:Åke Sandgren (HPC2N)

2011-09-29T06:53:02Z

Åke Sandgren (HPC2N):

{{application expert info
|first name=Åke
|last name=Sandgren
|centre=HPC2N
|fields=Computational science
|fte=50
|financing=SNIC
|other activities=


}}

HPC2N

2011-09-09T09:04:24Z

Åke Sandgren (HPC2N):

[[category:SNIC centre]]
High Performance Computing Center North (HPC2N) is located at Umeå University.

== List of resources ==
{{#ask: [[Category:Resource]] [[centre::{{PAGENAME}}]] |?description}}

== People ==
{{#ask: [[Category:person]] [[centre::{{PAGENAME}}]]
|mainlabel=-
|?image=
|?
|?role
|?field
|?expertise
}}

== Links ==
* [http://www.hpc2n.umu.se/ {{PAGENAME}} website]

VASP

2011-09-09T08:57:13Z

Åke Sandgren (HPC2N):

{{software info
|description=electronic structure calculation
|license=requires license
|fields=Computational materials science; Computational chemistry
|resources=kappa;matter;neolith;beda;akka;abisko
}}
The Vienna Ab initio Simulation Package ({{PAGENAME}}) is a program for performing {{#show: {{PAGENAME}} |?description}}. It is commonly used in the physics and materials science communities.

== Experts ==
{{list experts}}

== Availability ==
{{list resources for software}}

== License ==
{{show license}}

{{PAGENAME}} is not a "free" software. A valid {{PAGENAME}} license is required to be allowed to use it, even for centre provided installations.

== Links ==
* [http://cms.mpi.univie.ac.at/marsweb Main web page]. News about bug fixes and general information about VASP.
* [http://cms.mpi.univie.ac.at/vasp/vasp/vasp.html VASP online manual]. Find out what all those INCAR keyword means, what their default values are, etc.
* [http://cms.mpi.univie.ac.at/vasp-forum/forum.php The VASP forum]. For discussing "tricks of the VASP-trade", which knobs to turn, why results look strange, etc. To be able to post questions, you have to be registered and you need a VASP license.

SIESTA

2011-09-09T08:56:53Z

Åke Sandgren (HPC2N):

{{software info
|description=density-functional theory code for very large systems
|license=requires license
|fields=Computational materials science; Computational chemistry
|resources=kappa;matter;neolith;beda;akka
}}
[http://www.nanotec.es/products/siesta.php {{PAGENAME}}] (Spanish Initiative for Electronic Simulations with Thousands of Atoms) is a {{#show: {{PAGENAME}} |?description}} based on atomic orbital basis sets.

== Experts ==
{{list experts}}

== Availability ==
{{list resources for software}}

== License ==
{{show license}}

The SIESTA code is distributed under a "free for academic use"-license.

Quantum Espresso

2011-09-09T08:56:33Z

Åke Sandgren (HPC2N):

{{software info
|description=DFT based electronic structure modeling codes
|license=free
|fields=Computational materials science; Computational chemistry
|resources=beda;akka
}}
[http://www.quantum-espresso.org {{PAGENAME}}] (opEn Source Package for Research in Electronic Structure, Simulation, and Optimization) a {{#show: {{PAGENAME}} |?description}}.

== Experts ==
{{list experts}}

== Availability ==
{{list resources for software}}

== License ==
{{show license}}

The {{PAGENAME}} code is distributed under GPL.

OpenFOAM

2011-09-09T08:56:11Z

Åke Sandgren (HPC2N):

{{software info
|description=free, open source CFD software package by OpenCFD Ltd
|resources=beda,platon;akka
|license=free
|fields=Computational fluid dynamics
}}
The {{PAGENAME}} (Open Field Operation and Manipulation) CFD Toolbox is a {{#show: {{PAGENAME}} |?description}}. It has a large user base across most areas of engineering and science, from both commercial and academic organisations. OpenFOAM has an extensive range of features to solve anything from complex fluid flows involving chemical reactions, turbulence and heat transfer, to solid dynamics and electromagnetics.
OpenFOAM is supplied with numerous pre-configured solvers, utilities and libraries and so can be used like any typical simulation package. However, it is open, not only in terms of source code, but also in its structure and hierarchical design, so that its solvers, utilities and libraries are fully extensible.
OpenFOAM uses finite volume numerics to solve systems of partial differential equations ascribed on any 3D unstructured mesh of polyhedral cells. The fluid flow solvers are developed within a robust, implicit, pressure-velocity, iterative solution framework, although alternative techniques are applied to other continuum mechanics solvers. Domain decomposition parallelism is fundamental to the design of OpenFOAM and integrated at a low level so that solvers can generally be developed without the need for any ’parallel-specific’ coding.

== Experts ==
{{list experts}}

== Availability ==
{{list resources for software}}

== License ==
{{show license}}

== Links ==
* [http://www.openfoam.com/ OpenFOAM homepage]
* [http://www.openfoam.com/docs/user/ User guide (html)]
* [http://foam.sourceforge.net/docs/Guides-a4/UserGuide.pdf User guide (pdf)]

HMMER

2011-09-09T08:55:34Z

Åke Sandgren (HPC2N):

{{software info
|description=package for working with profile hidden Markov models (HMM)
|license=free
|fields=bioinformatics
|resources=kappa;matter;neolith;akka
}}
[http://hmmer.janelia.org {{PAGENAME}}] is a software {{#show: {{PAGENAME}} |?description}} of known regions in proteins.

== Experts ==
{{list experts}}

== General info ==

An HMM is a statistical model that describes the known sequence variations within a specific group of proteins that may be of special interest; for example a protein family with known function, or a domain containing a well studied interaction surface or an active site. HMM is a machine learning technique [http://en.wikipedia.org/wiki/Hidden_Markov_model] where the models are built from training examples that are known good members, and where the finished models can be used to reliably classify and annotate new or poorly understood protein sequences in an automated fashion. Large libraries of trusted HMMs (such as [http://pfam.sanger.ac.uk/ Pfam]) are of course immensely beneficial, as they can be used to automatically classify large portions of newly sequenced genomes, directly as they become available.

The HMMER package contains applications for working with HMMs, for example for:

* Building and calibrating HMMs.
* Matching an HMM against a sequence database (for finding new members).
* Matching a sequence against an HMM database (for finding new sequence features).

== Versions ==

There are two verions of HMMER that can conceivably be useful:

* HMMER-2.3.2: Old stable version.
* HMMER-3.0: Fast, but backwards incompatible and non-feature-complete.

Their implementations and output (and potentially also the actual results) are vastly different, so ongoing projects are not recommended to switch between them. For new project, it is highly recommended to spend some time to deduce which version is the most suitable.

HMMER-3 may seem like an obvious choice; it is much faster than its predecessor and it is currently used in large scale production (e.g. by [http://pfam.sanger.ac.uk/ Pfam]), and it is also promoted as the official main HMMER version. However, HMMER-3.0 is not feature complete. Especially, the old default alignment behavior (glocal, hmm_ls) is missing, so if this feature is necessary: choose HMMER-2.3.2.

== Computational considerations ==

=== Work locally ===

Many of the features in HMMER require access to database flatfiles, and standard practice when running a compute cluster is to copy all necessary files to a node local directory before any work is done with them. This behaviour is highly encouraged on most resources, since multiple simultaneous accesses to the same large files on a shared disk is likely to cause problems for all computations currently running on the resource, and not only for the owner of the badly behaving jobs. For this reason, most SNIC resources have amenities in place to aid you in running your HMMER jobs in an optimal manner (for example <code>prepare_db</code> and <code>$HMMER_DB_DIR</code>, described for example [https://extras.csc.fi/mgrid/hmmer_re/hmmer232/index.html here]).

=== Do not run out of memory ===

If possible, you should ensure that you have enough RAM to hold the database as well as the results and still have some headroom. This ensures that HMMER will not need to read data from disk unnecessarily, which otherwise would cause significant slowdown. This is less important with HMMER-2.3.2, since the HMM-sequence alignment implementation is so CPU intensive that memory and disk considerations are less likely to have an impact on runtime. Nevertheless, ensuring that the database files remain cached can be done for example by:

* '''Choose a system with enough RAM''' <br/> Multiprocessor systems generally have more memory than single processor systems, and the database will also require proportionally less memory, since only one copy is needed in the OS file cache regardless of the number of processors using it.
* '''Partition the search space''' <br/> For huge databases or very restricted amounts available memory it may be required to split the database into manageable chunks and process them as separate jobs.

=== Use your processors wisely ===

Users should not have to worry about this since the HMMER default behaviour is to run on all the CPU cores it can detect on the compute node, which is nearly always the most desirable. However, should you need to control this for any reason, the behaviour can be controlled by the <code>--ncpus</code> command line option, or the <code>$HMMER_NCPUS</code> environment variable, which should already be set to the correct value if you are using a preinstalled HMMER version on a SNIC resource.

== Compilation ==

Benchmarks at [http://www.nsc.liu.se NSC] have shown that Intel compilers seem to produce more efficient HMMER binaries than does gcc.

HMMER-2 is also extremely sensitive to hardware vectorisation optimisations, even to the extent that -xSSE4.2 produces significantly faster binaries than does -xSSE4.1, so it makes sense to set this as aggressively as possible. NSC uses icc 11.1.069 and <code>CFLAGS="-O3 -ip -xSSE4.2"</code> for the SNIC systems [http://www.nsc.liu.se/systems/snic/ Kappa] and [http://www.nsc.liu.se/systems/snic/ Matter], and <code>CFLAGS="-O3 -ip -xSSSE3"</code> for [http://www.nsc.liu.se/systems/snic/ Neolith].

The official binary distribution of HMMER-3.0 is compiled with icc, and is fully adequate for threaded operation. However, some of the HMMER-3 binaries (e.g. hmmscan) have been shown to perform upward of 50% better with MPI parallelisation, so this may constitute reason to recompile locally. It may also be profitable to carefully select MPI library, as intelmpi in standard configuration can give fluctuations in runtime upwards of +~100% with hmmsearch, while openmpi seemingly performs optimally and consistently. For HMMER-3, [http://www.nsc.liu.se NSC] uses icc 11.1.069 and openmpi 1.4.1, and uses the compilator flags automatically detected by the configure script.

== Availability ==
{{list resources for software}}

== License ==
{{show license}}

== Links ==
* [http://hmmer.janelia.org/ Official website]
* [ftp://selab.janelia.org/pub/software/hmmer3/3.0/Userguide.pdf HMMER-3 documentation]
* [http://selab.janelia.org/software/hmmer/2.3.2/hmmer-2.3.2.tar.gz HMMER-2.3.2 release] (contains pdf documentation)

Gnuplot

2011-09-09T08:55:17Z

Åke Sandgren (HPC2N):

{{software info
|description=portable command-line driven graphing utility
|fields=plotting utility
|license=free
|resources=kappa;matter;neolith;beda;platon;akka;abisko
}}
{{PAGENAME}} is a {{#show: {{PAGENAME}} |?description}}.

== Experts ==
{{list experts}}

== Availability ==
{{list resources for software}}

== License ==
{{show license}}

== Links ==
* [http://www.gnuplot.info/ Official website]
* [http://www.gnuplot.info/documentation.html Documentation index]