From ketan at ci.uchicago.edu Mon Nov 3 13:57:35 2014 From: ketan at ci.uchicago.edu (ketan at ci.uchicago.edu) Date: Mon, 3 Nov 2014 13:57:35 -0600 (CST) Subject: [Swift-commit] r8296 - SwiftApps/swift-galaxy Message-ID: <20141103195735.32B549D846@svn.ci.uchicago.edu> Author: ketan Date: 2014-11-03 13:57:33 -0600 (Mon, 03 Nov 2014) New Revision: 8296 Modified: SwiftApps/swift-galaxy/setup.py Log: small change to adjust to latest galaxy versions Modified: SwiftApps/swift-galaxy/setup.py =================================================================== --- SwiftApps/swift-galaxy/setup.py 2014-10-31 20:56:50 UTC (rev 8295) +++ SwiftApps/swift-galaxy/setup.py 2014-11-03 19:57:33 UTC (rev 8296) @@ -39,13 +39,13 @@ os.symlink ("/tmp/swift-galaxy/swift", galaxyloc+"/tools/swift"); #step 2. update the tool_conf.xml -tree = ET.parse(galaxyloc+"/tool_conf.xml") +tree = ET.parse(galaxyloc+"/config/tool_conf.xml.main") root = tree.getroot() if 'swift' not in root.attrib: root.append((ET.fromstring('
\n \n \n \n
\n '))) -tree.write (galaxyloc+"/tool_conf.xml") +tree.write (galaxyloc+"/config/tool_conf.xml.main") #step 3. Print message print "Swift/Galaxy Installed." From wozniak at ci.uchicago.edu Wed Nov 5 11:53:11 2014 From: wozniak at ci.uchicago.edu (wozniak at ci.uchicago.edu) Date: Wed, 5 Nov 2014 11:53:11 -0600 (CST) Subject: [Swift-commit] r8297 - www/main Message-ID: <20141105175311.933F79D8B5@svn.ci.uchicago.edu> Author: wozniak Date: 2014-11-05 11:53:09 -0600 (Wed, 05 Nov 2014) New Revision: 8297 Modified: www/main/index.php Log: WIP Modified: www/main/index.php =================================================================== --- www/main/index.php 2014-11-03 19:57:33 UTC (rev 8296) +++ www/main/index.php 2014-11-05 17:53:09 UTC (rev 8297) @@ -172,8 +172,15 @@

What's New

- +
+
Swift at SC 2014
+

Swift will be featured at:

+ + MTAGS +
+ +
Next Generation Swift

Swift/T runs millions of tasks per second on supercomputers.

From wozniak at ci.uchicago.edu Wed Nov 5 11:56:31 2014 From: wozniak at ci.uchicago.edu (wozniak at ci.uchicago.edu) Date: Wed, 5 Nov 2014 11:56:31 -0600 (CST) Subject: [Swift-commit] r8298 - www/main Message-ID: <20141105175631.293229D8B5@svn.ci.uchicago.edu> Author: wozniak Date: 2014-11-05 11:56:31 -0600 (Wed, 05 Nov 2014) New Revision: 8298 Modified: www/main/index.php Log: WIP Modified: www/main/index.php =================================================================== --- www/main/index.php 2014-11-05 17:53:09 UTC (rev 8297) +++ www/main/index.php 2014-11-05 17:56:31 UTC (rev 8298) @@ -175,9 +175,15 @@
Swift at SC 2014
-

Swift will be featured at:

- - MTAGS +

Swift will be featured at:
+ +

+

From wozniak at ci.uchicago.edu Wed Nov 5 12:05:30 2014 From: wozniak at ci.uchicago.edu (wozniak at ci.uchicago.edu) Date: Wed, 5 Nov 2014 12:05:30 -0600 (CST) Subject: [Swift-commit] r8299 - www/main Message-ID: <20141105180530.B7C199D8B5@svn.ci.uchicago.edu> Author: wozniak Date: 2014-11-05 12:05:30 -0600 (Wed, 05 Nov 2014) New Revision: 8299 Modified: www/main/index.php Log: SC participation Modified: www/main/index.php =================================================================== --- www/main/index.php 2014-11-05 17:56:31 UTC (rev 8298) +++ www/main/index.php 2014-11-05 18:05:30 UTC (rev 8299) @@ -174,15 +174,13 @@

What's New

-
Swift at SC 2014
-

Swift will be featured at:
- -

+
Swift at SC 2014
+

Swift will be featured in many events:
+ + Regular paper on Swift/T   
+ MTAGS
+ HPTCDL
+ ESPT

From ketan at ci.uchicago.edu Fri Nov 7 11:37:52 2014 From: ketan at ci.uchicago.edu (ketan at ci.uchicago.edu) Date: Fri, 7 Nov 2014 11:37:52 -0600 (CST) Subject: [Swift-commit] r8300 - SwiftApps/swift-galaxy/swift Message-ID: <20141107173752.3EE459D8B6@svn.ci.uchicago.edu> Author: ketan Date: 2014-11-07 11:37:52 -0600 (Fri, 07 Nov 2014) New Revision: 8300 Modified: SwiftApps/swift-galaxy/swift/buildsite.sh SwiftApps/swift-galaxy/swift/swiftforeach.xml Log: add config for Blues Modified: SwiftApps/swift-galaxy/swift/buildsite.sh =================================================================== --- SwiftApps/swift-galaxy/swift/buildsite.sh 2014-11-05 18:05:30 UTC (rev 8299) +++ SwiftApps/swift-galaxy/swift/buildsite.sh 2014-11-07 17:37:52 UTC (rev 8300) @@ -46,6 +46,25 @@ EOF ;; +blues ) +cat << EOF >> $wdir/pool.xml + + + + 4300 + 01:10:00 + 16 + 1 + 16 + 1 + 1 + 0.20 + 10000 + /tmp/swift.workdir + +EOF +;; + uc3 ) cat << EOF >> $wdir/pool.xml Modified: SwiftApps/swift-galaxy/swift/swiftforeach.xml =================================================================== --- SwiftApps/swift-galaxy/swift/swiftforeach.xml 2014-11-05 18:05:30 UTC (rev 8299) +++ SwiftApps/swift-galaxy/swift/swiftforeach.xml 2014-11-07 17:37:52 UTC (rev 8300) @@ -85,6 +85,7 @@ + From wozniak at ci.uchicago.edu Wed Nov 12 13:38:48 2014 From: wozniak at ci.uchicago.edu (wozniak at ci.uchicago.edu) Date: Wed, 12 Nov 2014 13:38:48 -0600 (CST) Subject: [Swift-commit] r8301 - www/Swift-T/downloads Message-ID: <20141112193848.3C2849D936@svn.ci.uchicago.edu> Author: wozniak Date: 2014-11-12 13:38:46 -0600 (Wed, 12 Nov 2014) New Revision: 8301 Added: www/Swift-T/downloads/exm-0.7.0.tar.gz Log: Adding Swift-T/downloads/exm-0.7.0.tar.gz Added: www/Swift-T/downloads/exm-0.7.0.tar.gz =================================================================== (Binary files differ) Property changes on: www/Swift-T/downloads/exm-0.7.0.tar.gz ___________________________________________________________________ Added: svn:mime-type + application/octet-stream From wozniak at ci.uchicago.edu Thu Nov 20 12:15:12 2014 From: wozniak at ci.uchicago.edu (wozniak at ci.uchicago.edu) Date: Thu, 20 Nov 2014 12:15:12 -0600 (CST) Subject: [Swift-commit] r8302 - www/Swift-T Message-ID: <20141120181512.C08EB9DB45@svn.ci.uchicago.edu> Author: wozniak Date: 2014-11-20 12:15:10 -0600 (Thu, 20 Nov 2014) New Revision: 8302 Modified: www/Swift-T/downloads.html Log: Swift/T release 0.7.0 Modified: www/Swift-T/downloads.html =================================================================== --- www/Swift-T/downloads.html 2014-11-12 19:38:46 UTC (rev 8301) +++ www/Swift-T/downloads.html 2014-11-20 18:15:10 UTC (rev 8302) @@ -535,6 +535,16 @@ } + +/* SWIFT/T GUIDE CUSTOMIZATIONS */ + +a:visited { + color: gray; +} +h5 { + font-size: 0.8em; +} + - + @@ -750,10 +760,78 @@
+

Series 0.7

+
+
+

Current/stable: 0.7.0

+
+

Changes:

+
    +
  • +

    +Support for remote execution via Coasters +

    +
  • +
  • +

    +New swift-t tool combines stc and turbine +

    +
  • +
  • +

    +New soft targeting feature for data-intensive computing +

    +
  • +
  • +

    +Ability to retry app functions +

    +
  • +
  • +

    +More features for TURBINE_OUTPUT +

    +
  • +
  • +

    +Default number of processes is now 2 (not 3) +

    +
  • +
  • +

    +Renamed aprun scheduler to cray +

    +
  • +
  • +

    +Renamed setup.sh to bootstrap +

    +
  • +
  • +

    +STC output is now in a *.tic file by default +

    +
  • +
+
+
+
+

Series 0.6

-

Current/stable: 0.6.1

+

0.6.1

  • @@ -1183,7 +1261,7 @@


    From wozniak at ci.uchicago.edu Thu Nov 20 14:45:39 2014 From: wozniak at ci.uchicago.edu (wozniak at ci.uchicago.edu) Date: Thu, 20 Nov 2014 14:45:39 -0600 (CST) Subject: [Swift-commit] r8303 - www/Swift-T Message-ID: <20141120204539.67BC59CCA2@svn.ci.uchicago.edu> Author: wozniak Date: 2014-11-20 14:45:39 -0600 (Thu, 20 Nov 2014) New Revision: 8303 Modified: www/Swift-T/turbine-sites.html Log: Updated Swift/T notes for BG/Q Modified: www/Swift-T/turbine-sites.html =================================================================== --- www/Swift-T/turbine-sites.html 2014-11-20 18:15:10 UTC (rev 8302) +++ www/Swift-T/turbine-sites.html 2014-11-20 20:45:39 UTC (rev 8303) @@ -746,8 +746,8 @@

    Turbine Sites Guide

    Justin M. Wozniak
    <wozniak at mcs.anl.gov>
    -version 0.6.1, -August 2014 +version 0.7.0, +November 2014
    Table of Contents
    @@ -894,7 +894,7 @@

    -turbine-aprun-run.zsh (PBS with Cray’s aprun) +turbine-cray-run.zsh (PBS with Cray’s aprun)

    @@ -910,22 +910,29 @@

    A typical invocation is:

    +
    swift-t -m pbs -n 96 -s settings.sh program.swift
    +
    +

    or:

    +
    +
    stc program.swift
    -turbine-pbs-run.zsh -n 96 -s settings.sh program.tcl
    +turbine-pbs-run.zsh -n 96 -s settings.sh program.tic
    -

    where program.tcl is the output of STC and settings.sh contains:

    +

    which are equivalent.

    +

    program.tic is the output of STC and settings.sh contains:

    export QUEUE=bigqueue
     export PPN=8
    -

    which would run program.tcl in 96 MPI processes on 12 nodes (8 +

    which would run program.tic in 96 MPI processes on 12 nodes (8 processes per node), submitted by PBS to queue bigqueue.

    Turbine scheduler variables

    For scheduled systems, Turbine accepts a common set of environment -variables.

    +variables. These may be placed in settings.sh or set by the user in +any other way.

    PROCS @@ -1073,7 +1080,7 @@

    Run standalone Turbine executable (created by mkstatic.tcl) instead of - program.tcl. + program.tic.

    @@ -1092,9 +1099,9 @@
    Tip
    When running on a big HPC machine, it may be difficult to get STC -(a Java-based program) running. STC output (program.tcl) is +(a Java-based program) running. STC output (program.tic) is platform-independent. You may run STC to develop and debug your -script on your local workstation, then simply copy program.tcl to +script on your local workstation, then simply copy program.tic to the big machine for execution. Just make sure that the STC and Turbine versions are compatible (the same release number). @@ -1115,7 +1122,7 @@ will pass it to mpiexec.

    -
    turbine -l -n 3 -f hosts.txt program.tcl
    +
    turbine -l -n 3 -f hosts.txt program.tic
@@ -1127,7 +1134,7 @@
echo crush.mcs.anl.gov >  hosts.txt
 echo crank.mcs.anl.gov >> hosts.txt
-turbine -l -n 3 -f hosts.txt program.tcl
+turbine -l -n 3 -f hosts.txt program.tic

Public installation

@@ -1188,7 +1195,7 @@
export TURBINE_LAUNCH_OPTS='-f hosts.txt'
-turbine -l -n 4 program.tcl
+turbine -l -n 4 program.tic
  • @@ -1226,7 +1233,7 @@

    To run:

    -
    srun ~wozniak/Public/turbine-0.1.1/scripts/submit/slurm/turbine-slurm.sh -n 3 ~/program.tcl
    +
    srun ~wozniak/Public/turbine-0.1.1/scripts/submit/slurm/turbine-slurm.sh -n 3 ~/program.tic
  • @@ -1308,7 +1315,7 @@
    export MODE=cluster
     export QUEUE=pubnet
     export PROJECT=...
    -turbine-cobalt-run.zsh -n 3 program.tcl
    +turbine-cobalt-run.zsh -n 3 program.tic
    @@ -1354,7 +1361,7 @@
    export QUEUE=batch
    -~wozniak/Public/turbine/scripts/submit/pbs/turbine-pbs-run.zsh -n 3 program.tcl
    +~wozniak/Public/turbine/scripts/submit/pbs/turbine-pbs-run.zsh -n 3 program.tic

    See the Turbine scheduler variables and Turbine run script options for additional settings.

    @@ -1417,7 +1424,7 @@

    To run:

    -
    ~wozniak/Public/turbine/scripts/submit/cobalt/turbine-cobalt-run.zsh -n 3 ~/program.tcl
    +
    ~wozniak/Public/turbine/scripts/submit/cobalt/turbine-cobalt-run.zsh -n 3 ~/program.tic
    @@ -1535,19 +1542,18 @@

    Blue Gene/Q

    -

    Vesta

    -
    -
    Public installation
    -

    As of: 0.4.0 - 07/29/2013

    +

    Mira/Cetus

    +

    As of: 0.7.0 - 11/20/2014

    +

    Add to PATH:

    • -STC: ~wozniak/Public/stc-bgq/bin/stc +STC: ~wozniak/Public/ppc64/stc/bin

    • -Turbine: ~wozniak/Public/turbine-bgq/scrips/submit/cobalt/turbine-cobalt-run.zsh +Turbine (optional): ~wozniak/Public/ppc64/turbine/scripts/submit/cobalt

    • @@ -1557,39 +1563,45 @@
      export MODE=BGQ
      -export QUEUE=<queue_name>
      -turbine-cobalt-run.zsh -n 3 program.tcl
      +export QUEUE=... +export PROJECT=... +swift-t -m cobalt -n 3 program.tic
    -

    The normal Turbine environment variables are honored, plus the -Turbine scheduler variables.

    -
    -

    Mira/Cetus

    -

    As of: 0.5.0 - 4/4/2014

    -

    Add to PATH: -* STC: wozniak/Public/ppc64/stc/bin -* Turbine: -wozniak/Public/ppc64/turbine/scripts/submit/cobalt

    +

    Vesta

    +

    As of: 0.7.0 - 11/20/2014

    • +STC: ~wozniak/Public/sfw/stc/bin +

      +
    • +
    • +

      +Turbine (optional): ~wozniak/Public/sfw/turbine/scripts/submit/turbine-cobalt-run.zsh +

      +
    • +
    • +

      Run as:

      export MODE=BGQ
      -export QUEUE=...
      -export PROJECT=...
      -turbine-cobalt-run.zsh -n 3 program.tcl
      +export QUEUE=default +swift-t -m cobalt -n 2 program.tic
    -
    -
    Build procedure
    -

    As of: 0.5.0 - 4/4/2014

    +

    The normal Turbine environment variables are honored, plus the +Turbine scheduler variables.

    +
    +
    +

    Build procedure

    +

    As of: 0.7.0 - 11/20/2014

    Tcl:

    The GCC installation does not support shared libraries. Thus, you must compile Tcl with bgxlc. You must modify the Makefile to use @@ -1598,22 +1610,32 @@

    You may get errors that say wrong digit. This is apparently a bgxlc bug when applied to Tcl’s StrToD.c. Compiling this file with -O3 fixes the problem.

    -

    Put /bgsys/drivers/V1R2M1/ppc64/comm/bin/gcc in your PATH.

    • -Compile c-utils with CC=/usr/bin/gcc +Compile c-utils with CC=powerpc64-bgq-linux-gcc

    • -Configure ADLB with CC=mpixlc --enable-mpi-2 --enable-xlc +Configure ADLB with CC=mpixlc --enable-mpi-2 --enable-xlc --disable-checkpoint

    • -Configure Turbine with CC=/usr/bin/gcc --disable-static --with-tcl=/home/wozniak/Public/sfw/ppc64/tcl-8.5.12 --with-mpi=/bgsys/drivers/V1R2M1/ppc64/comm --with-mpi-lib-name=mpich-gcc +Configure Turbine with:

      +
      +
      +
      CC=mpixlc
      +--disable-static
      +--with-tcl=/home/wozniak/Public/sfw/ppc64/bgxlc/dynamic/tcl-8.5.12
      +--with-mpi=/bgsys/drivers/V1R2M1/ppc64/comm
      +--with-mpi-lib-name=mpich-xl
      +--without-zlib
      +--without-hdf5
      +--disable-static-pkg
      +

    External scripting:

    @@ -1656,7 +1678,6 @@
    -

    Cray

    @@ -1664,7 +1685,7 @@

    Titan

    Titan is a Cray XK7 at the Oak Ridge Leadership Computing Facility.

    -

    Public installation

    +

    Public installation

    As of: 8/27/2014

    • @@ -2002,7 +2023,7 @@ NFS (including home directories). Thus, you must install Turbine and its libraries in /lustre. Also, your data must be in /lustre.

    -

    Public installation

    +

    Public installation

    Login nodes

    This installation is for use on the login node.

    @@ -2254,7 +2275,7 @@
    export TURBINE_LAUNCH_OPTS="-f $HOME/hosts.txt"
    -turbine program.tcl
    +turbine program.tic
    @@ -2283,8 +2304,8 @@

    From wozniak at ci.uchicago.edu Thu Nov 20 14:47:29 2014 From: wozniak at ci.uchicago.edu (wozniak at ci.uchicago.edu) Date: Thu, 20 Nov 2014 14:47:29 -0600 (CST) Subject: [Swift-commit] r8304 - www/Swift-T Message-ID: <20141120204729.C88639CCA2@svn.ci.uchicago.edu> Author: wozniak Date: 2014-11-20 14:47:29 -0600 (Thu, 20 Nov 2014) New Revision: 8304 Modified: www/Swift-T/turbine-sites.html Log: Minor update Modified: www/Swift-T/turbine-sites.html =================================================================== --- www/Swift-T/turbine-sites.html 2014-11-20 20:45:39 UTC (rev 8303) +++ www/Swift-T/turbine-sites.html 2014-11-20 20:47:29 UTC (rev 8304) @@ -857,7 +857,7 @@ script wrapper that configures Turbine and essentially runs:

    -
    mpiexec tclsh program.tcl
    +
    mpiexec tclsh program.tic

    On more complex, scheduled systems, users do not invoke mpiexec directly. Thus, sample scripts are provided below.

    @@ -2305,7 +2305,7 @@ From ketan at ci.uchicago.edu Sun Nov 23 18:50:37 2014 From: ketan at ci.uchicago.edu (ketan at ci.uchicago.edu) Date: Sun, 23 Nov 2014 18:50:37 -0600 (CST) Subject: [Swift-commit] r8305 - in SwiftApps: . ematter Message-ID: <20141124005037.9540C178884@svn.ci.uchicago.edu> Author: ketan Date: 2014-11-23 18:50:37 -0600 (Sun, 23 Nov 2014) New Revision: 8305 Added: SwiftApps/ematter/ SwiftApps/ematter/apps SwiftApps/ematter/cf SwiftApps/ematter/genfdf SwiftApps/ematter/lastlammpsdump2xyz.py SwiftApps/ematter/pasta SwiftApps/ematter/runbgq SwiftApps/ematter/runblues SwiftApps/ematter/sites.blues.xml SwiftApps/ematter/sites.cobalt-local.xml SwiftApps/ematter/sites.cobalt.xml SwiftApps/ematter/sites.local.xml SwiftApps/ematter/workflow.bgq.swift SwiftApps/ematter/workflow.blues.swift Log: adding ematter Added: SwiftApps/ematter/apps =================================================================== --- SwiftApps/ematter/apps (rev 0) +++ SwiftApps/ematter/apps 2014-11-24 00:50:37 UTC (rev 8305) @@ -0,0 +1,17 @@ +localhost cat /bin/cat null null null +localhost python /usr/bin/python null null null +localhost bash /bin/bash null null null +# +cluster bgsh /home/ketan/SwiftApps/subjobs/bg.sh null null null +cluster2 bgsh /home/ketan/SwiftApps/subjobs/bg.sh null null null +# +blues lammps lmp_linux null null null +blues smeagol /home/heinonen/smeagol-1.2-Feb-2014/smeagol-1.2_blues/Src/smeagol-1.2_csg null null null +blues bash /bin/bash null null null +blues python /soft/python/2.7.6/bin/python null null null +# +localblues lammps lmp_blues null null null +localblues smeagol /home/heinonen/smeagol-1.2-Feb-2014/smeagol-1.2_blues/Src/smeagol-1.2_csg null null null +localblues mpiexec mpiexec null null null +localblues bash /bin/bash null null null +localblues python /soft/python/2.7.6/bin/python null null null Added: SwiftApps/ematter/cf =================================================================== --- SwiftApps/ematter/cf (rev 0) +++ SwiftApps/ematter/cf 2014-11-24 00:50:37 UTC (rev 8305) @@ -0,0 +1,7 @@ +use.provider.staging=true +wrapperlog.always.transfer=false +execution.retries=0 +provider.staging.pin.swiftfiles=false +sitedir.keep=false +use.wrapper.staging=false + Added: SwiftApps/ematter/genfdf =================================================================== --- SwiftApps/ematter/genfdf (rev 0) +++ SwiftApps/ematter/genfdf 2014-11-24 00:50:37 UTC (rev 8305) @@ -0,0 +1,11 @@ +#!/bin/bash + +startrng=$1 +endrng=$2 +infdf=$3 + +for i in $(seq $startrng $endrng) +do +sed -e "s/VInitial[[:space:]]* 1.D0 eV/VInitial $i.D0 eV/" -e "s/VFinal[[:space:]]* 1.D0 eV/VFinal $i.D0 eV/" $infdf > $i.fdf +done + Property changes on: SwiftApps/ematter/genfdf ___________________________________________________________________ Added: svn:executable + * Added: SwiftApps/ematter/lastlammpsdump2xyz.py =================================================================== --- SwiftApps/ematter/lastlammpsdump2xyz.py (rev 0) +++ SwiftApps/ematter/lastlammpsdump2xyz.py 2014-11-24 00:50:37 UTC (rev 8305) @@ -0,0 +1,22 @@ +#!/usr/bin/env python + +# Set the import path to find the Pizza tools. +# Warning! Nonportable. + +import sys +sys.path.append('/home/ketan/pizza-2Jul14/src') +import dump, xyz + +if __name__ == '__main__': + # read the dump file (the first cl arg) + d = dump.dump(sys.argv[1]) + # Get array of times + t = d.time() + # Convert the list of dumped states to xyz (in memory) + x = xyz.xyz(d) + # Dump just the last time instance to a file (the second cl arg) + # This can be easily changed to use any other time slice between 0 + # and len(t)-1 inclusive. This will require additional validation + # of the additional input parameter, though. + x.single(t[-1],sys.argv[2]) + Property changes on: SwiftApps/ematter/lastlammpsdump2xyz.py ___________________________________________________________________ Added: svn:executable + * Added: SwiftApps/ematter/pasta =================================================================== --- SwiftApps/ematter/pasta (rev 0) +++ SwiftApps/ematter/pasta 2014-11-24 00:50:37 UTC (rev 8305) @@ -0,0 +1,17 @@ +#!/bin/bash + +filexyz=$1 +filefdf=$2 +fileresfdf=$3 +#extract after the last occurrence of Atom and move first column to last +tac $filexyz | sed -n '0,/^Atoms/p' | sed '$d' | tac | awk '{print $2, $3, $4, $1}' > tmp.extract + +#delete everything between the coordinates block +sed -i '/\%block AtomicCoordinatesAndAtomicSpecies/,/%endblock AtomicCoordinatesAndAtomicSpecies/{//!d}' $filefdf + +cp $filefdf $fileresfdf + +#insert the tmp.extract between the above patterns +sed -i '/\%block AtomicCoordinatesAndAtomicSpecies/ r tmp.extract' $fileresfdf + +echo "Pasta served" Property changes on: SwiftApps/ematter/pasta ___________________________________________________________________ Added: svn:executable + * Added: SwiftApps/ematter/runbgq =================================================================== --- SwiftApps/ematter/runbgq (rev 0) +++ SwiftApps/ematter/runbgq 2014-11-24 00:50:37 UTC (rev 8305) @@ -0,0 +1,4 @@ +#! /bin/sh + +/home/ketan/swift-0.95/cog/modules/swift/dist/swift-svn/bin/swift -sites.file sites.cobalt-local.xml -config cf -tc.file apps workflow.swift +#$HOME/swift-0.95-main/cog/modules/swift/dist/swift-svn/bin/swift -sites.file cobalt-local.xml -config cf -tc.file apps workflow.swift Property changes on: SwiftApps/ematter/runbgq ___________________________________________________________________ Added: svn:executable + * Added: SwiftApps/ematter/runblues =================================================================== --- SwiftApps/ematter/runblues (rev 0) +++ SwiftApps/ematter/runblues 2014-11-24 00:50:37 UTC (rev 8305) @@ -0,0 +1,4 @@ +#! /bin/sh + +/home/ketan/swift-0.95/cog/modules/swift/dist/swift-svn/bin/swift -sites.file sites.blues.xml -config cf -tc.file apps workflow.blues.swift +#$HOME/swift-0.95-main/cog/modules/swift/dist/swift-svn/bin/swift -sites.file cobalt-local.xml -config cf -tc.file apps workflow.swift Property changes on: SwiftApps/ematter/runblues ___________________________________________________________________ Added: svn:executable + * Added: SwiftApps/ematter/sites.blues.xml =================================================================== --- SwiftApps/ematter/sites.blues.xml (rev 0) +++ SwiftApps/ematter/sites.blues.xml 2014-11-24 00:50:37 UTC (rev 8305) @@ -0,0 +1,18 @@ + + + + + + 2300 + 00:20:00 + 16 + 1 + 16 + 1 + 1 + 0.20 + 10000 + /tmp/swift.workdir + + + Added: SwiftApps/ematter/sites.cobalt-local.xml =================================================================== --- SwiftApps/ematter/sites.cobalt-local.xml (rev 0) +++ SwiftApps/ematter/sites.cobalt-local.xml 2014-11-24 00:50:37 UTC (rev 8305) @@ -0,0 +1,38 @@ + + + + + + +1 +script + +0.99 +10000 +00:55:00 +3500 +3500 + +32 +32 +8 +DEBUG +TRUE +ON +/home/ketan/workerlogs +DEBUG +/home/ketan/workerlogs +4 + +/home/ketan/swiftwork + + + + + +/home/ketan/swiftwork +0.09 + + + + Added: SwiftApps/ematter/sites.cobalt.xml =================================================================== --- SwiftApps/ematter/sites.cobalt.xml (rev 0) +++ SwiftApps/ematter/sites.cobalt.xml 2014-11-24 00:50:37 UTC (rev 8305) @@ -0,0 +1,57 @@ + + + + + + +2 +script + +2.99 +10000 +00:40:00 +2050 + +64 +64 +8 +DEBUG +TRUE +ON +/home/ketan/workerlogs +DEBUG +/home/ketan/workerlogs +8 + +/home/ketan/swiftwork + + + + + + + +2 +script + +2.99 +10000 +00:40:00 +2050 + +64 +64 +8 +DEBUG +TRUE +ON +/home/ketan/workerlogs +DEBUG +/home/ketan/workerlogs +8 + +/home/ketan/swiftwork + + + + Added: SwiftApps/ematter/sites.local.xml =================================================================== --- SwiftApps/ematter/sites.local.xml (rev 0) +++ SwiftApps/ematter/sites.local.xml 2014-11-24 00:50:37 UTC (rev 8305) @@ -0,0 +1,13 @@ + + + + +09:55:00 +35000 +36000 +/home/ketan/swiftwork +0.09 + + + + Added: SwiftApps/ematter/workflow.bgq.swift =================================================================== --- SwiftApps/ematter/workflow.bgq.swift (rev 0) +++ SwiftApps/ematter/workflow.bgq.swift 2014-11-24 00:50:37 UTC (rev 8305) @@ -0,0 +1,131 @@ +type file; + +// Lammps app definition +app (file _dump, file _out, + file _err) lammps_app (string _lammps_exe, file _in, + file _geo, file _eam) +{ + bgsh _lammps_exe "-in" @_in stdout=@_out stderr=@_err; +} + +// Pizza app definition +app (file _xyz, file _out, file _err) pizza_app (file _pizza_src, file _dump) +{ + python @_pizza_src @_dump @_xyz stdout=@_out stderr=@_err; +} + +// Pasta app definition +app (file _fdf, file _out, file _err) pasta_app (file _pasta_src, file _xyz, file _fdf_tmp) +{ + bash @_pasta_src @_xyz @_fdf_tmp @_fdf stdout=@_out stderr=@_err; +} + +/* smeagol lead inputs +Au.psf Au.sic.psf input.fdf +O.psf O.sic.psf Ti.psf Ti.sic.psf */ + +//Smeagol lead app definition +app (file _au3dm, file _au3hst, + file _bulklft, file _bulkrgt, + file _out, file _err) smeagol_lead_app (string _smeagol_exe, file _aupsf, + file _ausicpsf, file _inputfdf, + file _opsf, file _osicpsf, + file _tipsf, file _tisicpsf) +{ + bgsh _smeagol_exe stdin=@_inputfdf stdout=@_out stderr=@_err; +} + +/* smeagol transport V0 inputs +Au3.DM Au3.HST Au.psf +Au.sic.psf bulklft.DAT bulkrgt.DAT +input.fdf O.psf O.sic.psf +Ti.psf Ti.sic.psf */ + +//Smeagol transport V0 app definition +app (file _tio2auhm, file _tio2audm, + file _out, file _err) smeagol_v0_app ( string _smeagol_exe, file _au3dm, + file _au3hst, file _aupsf, + file _ausicpsf, file _bulklft, + file _bulkrgt, file _inputfdf, + file _opsf, file _osicpsf, + file _tipsf, file _tisicpsf ) +{ + bgsh _smeagol_exe stdin=@_inputfdf stdout=@_out stderr=@_err; +} + +//Smeagol transport Vn app definition +//app () smeagol_vn_app (){} + +// Files +file lammps_in <"in.lammps">; +file lammps_geo <"AuTiO.geo">; +file lammps_eam <"Au_u3.eam">; + +file lammps_out <"out.lammps">; +file lammps_err <"err.lammps">; +file lammps_dump <"lammps.dump">; + +string lammps_exe="/soft/applications/lammps/24Apr13/lmp_bgq_xlomp"; + +//Invoke lammps +(lammps_dump, lammps_out, lammps_err) = lammps_app (lammps_exe, lammps_in, + lammps_geo, lammps_eam); + +file pizza_src<"lastlammpsdump2xyz.py">; + +file pizza_out <"out.pizza">; +file pizza_err <"err.pizza">; +file xyz <"forsmeagol.xyz">; + +//Invoke pizza +(xyz, pizza_out, pizza_err) = pizza_app(pizza_src, lammps_dump); + +file fdf_in<"input_leads.fdf">; + +file pasta_src<"pasta">; + +file smeagol_lead_out <"out.smeagol.lead">; +file smeagol_lead_err <"err.smeagol.lead">; +file au3dm <"Au3.DM">; +file au3hst <"Au3.HST">; +file bulklft <"bulklft.DAT">; +file bulkrgt <"bulkrgt.DAT">; + +file aupsf <"Au.psf">; +file ausicpsf <"Au.sic.psf">; +file opsf <"O.psf">; +file osicpsf <"O.sic.psf">; +file tipsf <"Ti.psf">; +file tisicpsf <"Ti.sic.psf">; + +string smeagol_exe="/gpfs/mira-fs1/projects/Oxygen_defects_ALCC/share/bin/smeagol-1.2_csg"; + +//Invoke smeagol lead +(au3dm, au3hst, + bulklft, bulkrgt, + smeagol_lead_out, + smeagol_lead_err) = smeagol_lead_app (smeagol_exe, aupsf, + ausicpsf, fdf_in, + opsf, osicpsf, + tipsf, tisicpsf); + +file fdf_v0<"input_t0.fdf">; +file fdf_proc<"input_proc_t0.fdf">; +file pasta_out<"out.pasta">; +file pasta_err<"err.pasta">; + +//Invoke pasta +(fdf_proc, pasta_out, pasta_err) = pasta_app(pasta_src, xyz, fdf_v0); + +file smeagol_transport_out<"out.smeagol_transport">; +file smeagol_transport_err<"err.smeagol_transport">; +file tio2auhm<"TiO2Au.HM">; +file tio2audm<"TiO2Au.DM">; +//Invoke smeagol transport V0 +(tio2auhm, tio2audm, + smeagol_transport_out, smeagol_transport_err) = smeagol_v0_app(smeagol_exe, au3dm, + au3hst, aupsf, ausicpsf, + bulklft, bulkrgt, + fdf_proc, opsf, osicpsf, + tipsf, tisicpsf); + Added: SwiftApps/ematter/workflow.blues.swift =================================================================== --- SwiftApps/ematter/workflow.blues.swift (rev 0) +++ SwiftApps/ematter/workflow.blues.swift 2014-11-24 00:50:37 UTC (rev 8305) @@ -0,0 +1,147 @@ +type file; + +// Lammps app definition +app (file _dump) lammps_app (file _in, + file _geo, file _eam) +{ + lammps "-in" @_in stdout=@_out stderr=@_err; +} + +// Pizza app definition +app (file _xyz) pizza_app (file _pizza_src, file _dump) +{ + python @_pizza_src @_dump @_xyz stdout=@_out stderr=@_err; +} + +// Pasta app definition +app (file _fdf) pasta_app (file _pasta_src, file _xyz, file _fdf_tmp) +{ + bash @_pasta_src @_xyz @_fdf_tmp @_fdf; +} + +/* smeagol lead inputs +Au.psf Au.sic.psf input.fdf +O.psf O.sic.psf Ti.psf Ti.sic.psf */ + +//Smeagol lead app definition +app (file _au3dm, file _au3hst, + file _bulklft, file _bulkrgt, + file _out) smeagol_lead_app (file _aupsf, + file _ausicpsf, file _inputfdf, + file _opsf, file _osicpsf, + file _tipsf, file _tisicpsf) +{ + //smeagol stdin=@_inputfdf stdout=@_out stderr=@_err; + mpiexec "/home/heinonen/smeagol-1.2-Feb-2014/smeagol-1.2_blues/Src/smeagol-1.2_csg" stdin=@_inputfdf stdout=@_out stderr=@_err; +} + +/* smeagol transport V0 inputs +Au3.DM Au3.HST Au.psf +Au.sic.psf bulklft.DAT bulkrgt.DAT +input.fdf O.psf O.sic.psf +Ti.psf Ti.sic.psf */ + +//Smeagol transport V0 app definition +app (file _tio2auhm, file _tio2audm, + file _out) smeagol_v0_app ( file _au3dm, + file _au3hst, file _aupsf, + file _ausicpsf, file _bulklft, + file _bulkrgt, file _inputfdf, + file _opsf, file _osicpsf, + file _tipsf, file _tisicpsf ) +{ + //smeagol stdin=@_inputfdf stdout=@_out stderr=@_err; + mpiexec "/home/heinonen/smeagol-1.2-Feb-2014/smeagol-1.2_blues/Src/smeagol-1.2_csg" stdin=@_inputfdf stdout=@_out stderr=@_err; +} + +app (file[] _fdf) gen_fdf(file _infdf, int _rstart, int _rend){ + genfdf _rstart _rend @_infdf; +} + + +//Smeagol transport Vn app definition +app (file _out) smeagol_vn_app ( file _au3dm, + file _au3hst, file _aupsf, + file _ausicpsf, file _bulklft, + file _bulkrgt, file _inputfdf, + file _opsf, file _osicpsf, + file _tipsf, file _tisicpsf ){ + + mpiexec "/home/heinonen/smeagol-1.2-Feb-2014/smeagol-1.2_blues/Src/smeagol-1.2_csg" stdin=@_inputfdf stdout=@_out stderr=@_err; +} + +// Files +file lammps_in <"in.lammps">; +file lammps_geo <"AuTiO.geo">; +file lammps_eam <"Au_u3.eam">; + +file lammps_dump <"lammps.dump">; + +//Invoke lammps +(lammps_dump) = lammps_app (lammps_in, + lammps_geo, lammps_eam); + +file pizza_src<"lastlammpsdump2xyz.py">; + +file xyz <"forsmeagol.xyz">; + +//Invoke pizza +(xyz) = pizza_app(pizza_src, lammps_dump); + +file fdf_in<"input_leads.fdf">; + +file pasta_src<"pasta">; + +file smeagol_lead_out <"out.smeagol.lead">; +file au3dm <"Au3.DM">; +file au3hst <"Au3.HST">; +file bulklft <"bulklft.DAT">; +file bulkrgt <"bulkrgt.DAT">; + +file aupsf <"Au.psf">; +file ausicpsf <"Au.sic.psf">; +file opsf <"O.psf">; +file osicpsf <"O.sic.psf">; +file tipsf <"Ti.psf">; +file tisicpsf <"Ti.sic.psf">; + +//Invoke smeagol lead +(au3dm, au3hst, + bulklft, bulkrgt, + smeagol_lead_out) = smeagol_lead_app (aupsf, ausicpsf, fdf_in, + opsf, osicpsf, + tipsf, tisicpsf); + +file fdf_v0<"input_t0.fdf">; +file smeagol_transport_out<"out.smeagol_transport">; +file tio2auhm<"TiO2Au.HM">; +file tio2audm<"TiO2Au.DM">; + +//Invoke smeagol transport V0 +(tio2auhm, tio2audm, + smeagol_transport_out) = smeagol_v0_app(au3dm, au3hst, + aupsf, ausicpsf, + bulklft, bulkrgt, + fdf_v0, opsf, osicpsf, + tipsf, tisicpsf); + + +file fdf_v1<"input_t1.fdf">; +file fdf_proc_v1<"input_proc_t1.fdf">; + +//Invoke pasta +(fdf_proc_v1) = pasta_app(pasta_src, xyz, fdf_v1); + +file smeagol_transport_out2<"out.smeagol_transport2">; + +int rstart=1; +int rend=2; +foreach i in [rstart:rend] +{ + +(smeagol_transport_out2) = smeagol_vn_app(au3dm, au3hst, + aupsf, ausicpsf, + bulklft, bulkrgt, + fdf_proc_v1, opsf, osicpsf, + tipsf, tisicpsf); +} From ketan at ci.uchicago.edu Mon Nov 24 12:38:28 2014 From: ketan at ci.uchicago.edu (ketan at ci.uchicago.edu) Date: Mon, 24 Nov 2014 12:38:28 -0600 (CST) Subject: [Swift-commit] r8306 - SwiftApps/ematter Message-ID: <20141124183828.ECF129DB45@svn.ci.uchicago.edu> Author: ketan Date: 2014-11-24 12:38:28 -0600 (Mon, 24 Nov 2014) New Revision: 8306 Modified: SwiftApps/ematter/apps SwiftApps/ematter/genfdf SwiftApps/ematter/workflow.blues.swift Log: comments in swift source Modified: SwiftApps/ematter/apps =================================================================== --- SwiftApps/ematter/apps 2014-11-24 00:50:37 UTC (rev 8305) +++ SwiftApps/ematter/apps 2014-11-24 18:38:28 UTC (rev 8306) @@ -9,9 +9,11 @@ blues smeagol /home/heinonen/smeagol-1.2-Feb-2014/smeagol-1.2_blues/Src/smeagol-1.2_csg null null null blues bash /bin/bash null null null blues python /soft/python/2.7.6/bin/python null null null +blues genfdf /home/ketan/ematter/smallrun/swift null null null # localblues lammps lmp_blues null null null localblues smeagol /home/heinonen/smeagol-1.2-Feb-2014/smeagol-1.2_blues/Src/smeagol-1.2_csg null null null localblues mpiexec mpiexec null null null localblues bash /bin/bash null null null localblues python /soft/python/2.7.6/bin/python null null null +localblues genfdf /home/ketan/ematter/smallrun/swift/genfdf null null null Modified: SwiftApps/ematter/genfdf =================================================================== --- SwiftApps/ematter/genfdf 2014-11-24 00:50:37 UTC (rev 8305) +++ SwiftApps/ematter/genfdf 2014-11-24 18:38:28 UTC (rev 8306) @@ -1,11 +1,7 @@ #!/bin/bash -startrng=$1 -endrng=$2 -infdf=$3 +i=$1 +infdf=$2 -for i in $(seq $startrng $endrng) -do -sed -e "s/VInitial[[:space:]]* 1.D0 eV/VInitial $i.D0 eV/" -e "s/VFinal[[:space:]]* 1.D0 eV/VFinal $i.D0 eV/" $infdf > $i.fdf -done +sed -e "s/VInitial[[:space:]]* 1.D0 eV/VInitial $i.D0 eV/" -e "s/VFinal[[:space:]]* 1.D0 eV/VFinal $i.D0 eV/" $infdf Modified: SwiftApps/ematter/workflow.blues.swift =================================================================== --- SwiftApps/ematter/workflow.blues.swift 2014-11-24 00:50:37 UTC (rev 8305) +++ SwiftApps/ematter/workflow.blues.swift 2014-11-24 18:38:28 UTC (rev 8306) @@ -1,93 +1,87 @@ type file; -// Lammps app definition -app (file _dump) lammps_app (file _in, - file _geo, file _eam) +/* == Lammps app definition == */ +app (file _dump) lammps_app (file _in, file _geo, file _eam) { - lammps "-in" @_in stdout=@_out stderr=@_err; + lammps "-in" @_in; } -// Pizza app definition +/* == Pizza app definition == */ app (file _xyz) pizza_app (file _pizza_src, file _dump) { - python @_pizza_src @_dump @_xyz stdout=@_out stderr=@_err; + python @_pizza_src @_dump @_xyz; } -// Pasta app definition +/* == Pasta app definition == */ app (file _fdf) pasta_app (file _pasta_src, file _xyz, file _fdf_tmp) { bash @_pasta_src @_xyz @_fdf_tmp @_fdf; } -/* smeagol lead inputs +/* == +smeagol lead inputs Au.psf Au.sic.psf input.fdf -O.psf O.sic.psf Ti.psf Ti.sic.psf */ +O.psf O.sic.psf Ti.psf Ti.sic.psf +== */ -//Smeagol lead app definition +/* == Smeagol lead app definition == */ app (file _au3dm, file _au3hst, file _bulklft, file _bulkrgt, - file _out) smeagol_lead_app (file _aupsf, - file _ausicpsf, file _inputfdf, - file _opsf, file _osicpsf, - file _tipsf, file _tisicpsf) + file _out) smeagol_lead_app (file _aupsf, file _ausicpsf, + file _inputfdf, file _opsf, + file _osicpsf, file _tipsf, + file _tisicpsf) { - //smeagol stdin=@_inputfdf stdout=@_out stderr=@_err; - mpiexec "/home/heinonen/smeagol-1.2-Feb-2014/smeagol-1.2_blues/Src/smeagol-1.2_csg" stdin=@_inputfdf stdout=@_out stderr=@_err; + mpiexec "/home/heinonen/smeagol-1.2-Feb-2014/smeagol-1.2_blues/Src/smeagol-1.2_csg" stdin=@_inputfdf stdout=@_out; } -/* smeagol transport V0 inputs +/* == +smeagol transport V0 inputs Au3.DM Au3.HST Au.psf Au.sic.psf bulklft.DAT bulkrgt.DAT input.fdf O.psf O.sic.psf -Ti.psf Ti.sic.psf */ +Ti.psf Ti.sic.psf +== */ -//Smeagol transport V0 app definition +/* == Smeagol transport V0 app definition == */ app (file _tio2auhm, file _tio2audm, - file _out) smeagol_v0_app ( file _au3dm, - file _au3hst, file _aupsf, - file _ausicpsf, file _bulklft, - file _bulkrgt, file _inputfdf, - file _opsf, file _osicpsf, - file _tipsf, file _tisicpsf ) + file _out) smeagol_v0_app ( file _au3dm, file _au3hst, file _aupsf, + file _ausicpsf, file _bulklft, file _bulkrgt, + file _inputfdf, file _opsf, file _osicpsf, + file _tipsf, file _tisicpsf ) { - //smeagol stdin=@_inputfdf stdout=@_out stderr=@_err; - mpiexec "/home/heinonen/smeagol-1.2-Feb-2014/smeagol-1.2_blues/Src/smeagol-1.2_csg" stdin=@_inputfdf stdout=@_out stderr=@_err; + mpiexec "/home/heinonen/smeagol-1.2-Feb-2014/smeagol-1.2_blues/Src/smeagol-1.2_csg" stdin=@_inputfdf stdout=@_out; } -app (file[] _fdf) gen_fdf(file _infdf, int _rstart, int _rend){ - genfdf _rstart _rend @_infdf; +/* == Generate fdfs app definition == */ +app (file _fdf) gen_fdf(int _r, file _infdf) +{ + genfdf _r @_infdf stdout=@_fdf; } -//Smeagol transport Vn app definition +/* == Smeagol transport Vn app definition == */ app (file _out) smeagol_vn_app ( file _au3dm, file _au3hst, file _aupsf, file _ausicpsf, file _bulklft, file _bulkrgt, file _inputfdf, file _opsf, file _osicpsf, - file _tipsf, file _tisicpsf ){ - - mpiexec "/home/heinonen/smeagol-1.2-Feb-2014/smeagol-1.2_blues/Src/smeagol-1.2_csg" stdin=@_inputfdf stdout=@_out stderr=@_err; + file _tipsf, file _tisicpsf ) +{ + mpiexec "/home/heinonen/smeagol-1.2-Feb-2014/smeagol-1.2_blues/Src/smeagol-1.2_csg" stdin=@_inputfdf stdout=@_out; } -// Files +/* == Input and output files definition and mappings == */ file lammps_in <"in.lammps">; file lammps_geo <"AuTiO.geo">; file lammps_eam <"Au_u3.eam">; file lammps_dump <"lammps.dump">; -//Invoke lammps -(lammps_dump) = lammps_app (lammps_in, - lammps_geo, lammps_eam); - file pizza_src<"lastlammpsdump2xyz.py">; file xyz <"forsmeagol.xyz">; -//Invoke pizza -(xyz) = pizza_app(pizza_src, lammps_dump); - file fdf_in<"input_leads.fdf">; file pasta_src<"pasta">; @@ -105,19 +99,39 @@ file tipsf <"Ti.psf">; file tisicpsf <"Ti.sic.psf">; -//Invoke smeagol lead + +file fdf_v0<"input_t0.fdf">; +file smeagol_transport_out<"out.smeagol_transport">; +file tio2auhm<"TiO2Au.HM">; +file tio2audm<"TiO2Au.DM">; + +file fdf_v1<"input_t1.fdf">; +file fdf_proc_v1<"input_proc_t1.fdf">; + + +file smeagol_transport_outn[]; + +int rstart=1; +int rend=2; +file fdf_proc_vn[]; + +/* == Invoke lammps == */ +(lammps_dump) = lammps_app (lammps_in, lammps_geo, lammps_eam); + +/* == Invoke pizza == */ +(xyz) = pizza_app(pizza_src, lammps_dump); + + +/* == Invoke smeagol lead == */ (au3dm, au3hst, bulklft, bulkrgt, smeagol_lead_out) = smeagol_lead_app (aupsf, ausicpsf, fdf_in, opsf, osicpsf, tipsf, tisicpsf); -file fdf_v0<"input_t0.fdf">; -file smeagol_transport_out<"out.smeagol_transport">; -file tio2auhm<"TiO2Au.HM">; -file tio2audm<"TiO2Au.DM">; -//Invoke smeagol transport V0 +/* == Invoke smeagol transport V0 == */ (tio2auhm, tio2audm, smeagol_transport_out) = smeagol_v0_app(au3dm, au3hst, aupsf, ausicpsf, @@ -125,23 +139,24 @@ fdf_v0, opsf, osicpsf, tipsf, tisicpsf); +/* == Invoke pasta == */ +(fdf_proc_v1) = pasta_app(pasta_src, xyz, fdf_v1); -file fdf_v1<"input_t1.fdf">; -file fdf_proc_v1<"input_proc_t1.fdf">; -//Invoke pasta -(fdf_proc_v1) = pasta_app(pasta_src, xyz, fdf_v1); +/* == +In a parallel 'foreach' loop, invoke gen_fdf and smeagol for the n V calculations +== */ -file smeagol_transport_out2<"out.smeagol_transport2">; - -int rstart=1; -int rend=2; foreach i in [rstart:rend] { -(smeagol_transport_out2) = smeagol_vn_app(au3dm, au3hst, +fdf_proc_vn[i]=gen_fdf(i,fdf_proc_v1); + +(smeagol_transport_outn[i]) = smeagol_vn_app(au3dm, au3hst, aupsf, ausicpsf, bulklft, bulkrgt, - fdf_proc_v1, opsf, osicpsf, - tipsf, tisicpsf); + fdf_proc_vn[i], opsf, + osicpsf, tipsf, + tisicpsf); } + From ketan at ci.uchicago.edu Mon Nov 24 13:37:55 2014 From: ketan at ci.uchicago.edu (ketan at ci.uchicago.edu) Date: Mon, 24 Nov 2014 13:37:55 -0600 (CST) Subject: [Swift-commit] r8307 - SwiftApps/ematter Message-ID: <20141124193755.5E2A09DA98@svn.ci.uchicago.edu> Author: ketan Date: 2014-11-24 13:37:55 -0600 (Mon, 24 Nov 2014) New Revision: 8307 Modified: SwiftApps/ematter/workflow.blues.swift Log: improve readability' Modified: SwiftApps/ematter/workflow.blues.swift =================================================================== --- SwiftApps/ematter/workflow.blues.swift 2014-11-24 18:38:28 UTC (rev 8306) +++ SwiftApps/ematter/workflow.blues.swift 2014-11-24 19:37:55 UTC (rev 8307) @@ -75,47 +75,45 @@ file lammps_in <"in.lammps">; file lammps_geo <"AuTiO.geo">; file lammps_eam <"Au_u3.eam">; - file lammps_dump <"lammps.dump">; file pizza_src<"lastlammpsdump2xyz.py">; +file pasta_src<"pasta">; file xyz <"forsmeagol.xyz">; file fdf_in<"input_leads.fdf">; +file fdf_v0<"input_t0.fdf">; +file fdf_v1<"input_t1.fdf">; +file fdf_proc_v1<"input_proc_t1.fdf">; -file pasta_src<"pasta">; - file smeagol_lead_out <"out.smeagol.lead">; file au3dm <"Au3.DM">; file au3hst <"Au3.HST">; -file bulklft <"bulklft.DAT">; -file bulkrgt <"bulkrgt.DAT">; - file aupsf <"Au.psf">; file ausicpsf <"Au.sic.psf">; file opsf <"O.psf">; file osicpsf <"O.sic.psf">; file tipsf <"Ti.psf">; file tisicpsf <"Ti.sic.psf">; +file smeagol_transport_out<"out.smeagol_transport">; +file bulklft <"bulklft.DAT">; +file bulkrgt <"bulkrgt.DAT">; -file fdf_v0<"input_t0.fdf">; -file smeagol_transport_out<"out.smeagol_transport">; file tio2auhm<"TiO2Au.HM">; file tio2audm<"TiO2Au.DM">; -file fdf_v1<"input_t1.fdf">; -file fdf_proc_v1<"input_proc_t1.fdf">; - - file smeagol_transport_outn[]; -int rstart=1; -int rend=2; file fdf_proc_vn[]; +int Vstart=1; +int Vend=2; + +/* == End files and variable declaration == */ + /* == Invoke lammps == */ (lammps_dump) = lammps_app (lammps_in, lammps_geo, lammps_eam); @@ -147,9 +145,9 @@ In a parallel 'foreach' loop, invoke gen_fdf and smeagol for the n V calculations == */ -foreach i in [rstart:rend] +foreach i in [Vstart:Vend] { - +/* == generate fdfs for different voltages == */ fdf_proc_vn[i]=gen_fdf(i,fdf_proc_v1); (smeagol_transport_outn[i]) = smeagol_vn_app(au3dm, au3hst, From ketan at ci.uchicago.edu Mon Nov 24 20:34:48 2014 From: ketan at ci.uchicago.edu (ketan at ci.uchicago.edu) Date: Mon, 24 Nov 2014 20:34:48 -0600 (CST) Subject: [Swift-commit] r8308 - SwiftApps/ematter Message-ID: <20141125023448.E275B9DB45@svn.ci.uchicago.edu> Author: ketan Date: 2014-11-24 20:34:48 -0600 (Mon, 24 Nov 2014) New Revision: 8308 Modified: SwiftApps/ematter/pasta SwiftApps/ematter/workflow.blues.swift Log: _ Modified: SwiftApps/ematter/pasta =================================================================== --- SwiftApps/ematter/pasta 2014-11-24 19:37:55 UTC (rev 8307) +++ SwiftApps/ematter/pasta 2014-11-25 02:34:48 UTC (rev 8308) @@ -4,8 +4,11 @@ filefdf=$2 fileresfdf=$3 #extract after the last occurrence of Atom and move first column to last -tac $filexyz | sed -n '0,/^Atoms/p' | sed '$d' | tac | awk '{print $2, $3, $4, $1}' > tmp.extract +tac $filexyz | sed -n '0,/^Atoms/p' | sed '$d' | tac | awk '{print $2, $3, $4, $1}' > 1.tmp +grep "0.0 0.0 0.0\|0.0 0.0 2.5\|0.0 0.0 5.0\|0.0 0.0 7.5" 1.tmp > tmp.extract +grep -v "0.0 0.0 0.0\|0.0 0.0 2.5\|0.0 0.0 5.0\|0.0 0.0 7.5" 1.tmp >> tmp.extract + #delete everything between the coordinates block sed -i '/\%block AtomicCoordinatesAndAtomicSpecies/,/%endblock AtomicCoordinatesAndAtomicSpecies/{//!d}' $filefdf Modified: SwiftApps/ematter/workflow.blues.swift =================================================================== --- SwiftApps/ematter/workflow.blues.swift 2014-11-24 19:37:55 UTC (rev 8307) +++ SwiftApps/ematter/workflow.blues.swift 2014-11-25 02:34:48 UTC (rev 8308) @@ -54,7 +54,7 @@ } /* == Generate fdfs app definition == */ -app (file _fdf) gen_fdf(int _r, file _infdf) +app (file _fdf) gen_fdf(float _r, file _infdf) { genfdf _r @_infdf stdout=@_fdf; } @@ -75,6 +75,7 @@ file lammps_in <"in.lammps">; file lammps_geo <"AuTiO.geo">; file lammps_eam <"Au_u3.eam">; + file lammps_dump <"lammps.dump">; file pizza_src<"lastlammpsdump2xyz.py">; @@ -109,8 +110,10 @@ file fdf_proc_vn[]; -int Vstart=1; -int Vend=2; +float Vstart=0.1; +float Vend=1.0; +float Vstep=0.1; +float Vs[]=[0.1,0.2,0.3,0.4,0.5,0.6,0.7,0.8,0.9,1.0]; /* == End files and variable declaration == */ @@ -145,10 +148,10 @@ In a parallel 'foreach' loop, invoke gen_fdf and smeagol for the n V calculations == */ -foreach i in [Vstart:Vend] +foreach v,i in Vs { /* == generate fdfs for different voltages == */ -fdf_proc_vn[i]=gen_fdf(i,fdf_proc_v1); +fdf_proc_vn[i]=gen_fdf(v,fdf_proc_v1); (smeagol_transport_outn[i]) = smeagol_vn_app(au3dm, au3hst, aupsf, ausicpsf, From ketan at ci.uchicago.edu Tue Nov 25 09:42:33 2014 From: ketan at ci.uchicago.edu (ketan at ci.uchicago.edu) Date: Tue, 25 Nov 2014 09:42:33 -0600 (CST) Subject: [Swift-commit] r8309 - SwiftApps/ematter Message-ID: <20141125154233.2E5159D8B8@svn.ci.uchicago.edu> Author: ketan Date: 2014-11-25 09:42:32 -0600 (Tue, 25 Nov 2014) New Revision: 8309 Modified: SwiftApps/ematter/genfdf SwiftApps/ematter/workflow.blues.swift Log: float index type Modified: SwiftApps/ematter/genfdf =================================================================== --- SwiftApps/ematter/genfdf 2014-11-25 02:34:48 UTC (rev 8308) +++ SwiftApps/ematter/genfdf 2014-11-25 15:42:32 UTC (rev 8309) @@ -3,5 +3,5 @@ i=$1 infdf=$2 -sed -e "s/VInitial[[:space:]]* 1.D0 eV/VInitial $i.D0 eV/" -e "s/VFinal[[:space:]]* 1.D0 eV/VFinal $i.D0 eV/" $infdf +sed -e "s/VInitial[[:space:]]* 1.D0 eV/VInitial $i eV/" -e "s/VFinal[[:space:]]* 1.D0 eV/VFinal $i eV/" $infdf Modified: SwiftApps/ematter/workflow.blues.swift =================================================================== --- SwiftApps/ematter/workflow.blues.swift 2014-11-25 02:34:48 UTC (rev 8308) +++ SwiftApps/ematter/workflow.blues.swift 2014-11-25 15:42:32 UTC (rev 8309) @@ -1,5 +1,19 @@ +/* == +This is a Swift workflow script for the ematter application. The script contains the following parts: + +-- A one-line type declaration +-- App function definitions +-- Input files and variables definitions +-- Output files definitions +-- Invocation of app functions +== */ + + type file; + +/* == App function definitions == */ + /* == Lammps app definition == */ app (file _dump) lammps_app (file _in, file _geo, file _eam) { @@ -59,7 +73,6 @@ genfdf _r @_infdf stdout=@_fdf; } - /* == Smeagol transport Vn app definition == */ app (file _out) smeagol_vn_app ( file _au3dm, file _au3hst, file _aupsf, @@ -71,32 +84,33 @@ mpiexec "/home/heinonen/smeagol-1.2-Feb-2014/smeagol-1.2_blues/Src/smeagol-1.2_csg" stdin=@_inputfdf stdout=@_out; } -/* == Input and output files definition and mappings == */ +/* == Input files definitions == */ file lammps_in <"in.lammps">; file lammps_geo <"AuTiO.geo">; file lammps_eam <"Au_u3.eam">; -file lammps_dump <"lammps.dump">; +file fdf_leads<"input_leads.fdf">; +file fdf_v0<"input_t0.fdf">; +file aupsf <"Au.psf">; +file ausicpsf <"Au.sic.psf">; +file opsf <"O.psf">; +file osicpsf <"O.sic.psf">; +file tipsf <"Ti.psf">; +file tisicpsf <"Ti.sic.psf">; + file pizza_src<"lastlammpsdump2xyz.py">; file pasta_src<"pasta">; + +/* == Output files definitions == */ file xyz <"forsmeagol.xyz">; +file lammps_dump <"lammps.dump">; +file fdf_proc<"input_proc.fdf">; -file fdf_in<"input_leads.fdf">; -file fdf_v0<"input_t0.fdf">; -file fdf_v1<"input_t1.fdf">; -file fdf_proc_v1<"input_proc_t1.fdf">; - file smeagol_lead_out <"out.smeagol.lead">; file au3dm <"Au3.DM">; file au3hst <"Au3.HST">; -file aupsf <"Au.psf">; -file ausicpsf <"Au.sic.psf">; -file opsf <"O.psf">; -file osicpsf <"O.sic.psf">; -file tipsf <"Ti.psf">; -file tisicpsf <"Ti.sic.psf">; file smeagol_transport_out<"out.smeagol_transport">; file bulklft <"bulklft.DAT">; @@ -105,13 +119,14 @@ file tio2auhm<"TiO2Au.HM">; file tio2audm<"TiO2Au.DM">; -file smeagol_transport_outn[]; -file fdf_proc_vn[]; +file[float] fdf_proc_vn; -float Vstart=0.1; -float Vend=1.0; +float Vstart=0.1; /*== Change this value to change the starting voltage ==*/ +float Vend=1.0; /*== Change this value to change the ending voltage ==*/ + float Vstep=0.1; float Vs[]=[0.1,0.2,0.3,0.4,0.5,0.6,0.7,0.8,0.9,1.0]; @@ -127,7 +142,7 @@ /* == Invoke smeagol lead == */ (au3dm, au3hst, bulklft, bulkrgt, - smeagol_lead_out) = smeagol_lead_app (aupsf, ausicpsf, fdf_in, + smeagol_lead_out) = smeagol_lead_app (aupsf, ausicpsf, fdf_leads, opsf, osicpsf, tipsf, tisicpsf); @@ -141,17 +156,17 @@ tipsf, tisicpsf); /* == Invoke pasta == */ -(fdf_proc_v1) = pasta_app(pasta_src, xyz, fdf_v1); +(fdf_proc) = pasta_app(pasta_src, xyz, fdf_v0); /* == In a parallel 'foreach' loop, invoke gen_fdf and smeagol for the n V calculations == */ -foreach v,i in Vs +foreach i in [Vstart:Vend:Vstep] { /* == generate fdfs for different voltages == */ -fdf_proc_vn[i]=gen_fdf(v,fdf_proc_v1); +fdf_proc_vn[i]=gen_fdf(i,fdf_proc); (smeagol_transport_outn[i]) = smeagol_vn_app(au3dm, au3hst, aupsf, ausicpsf, From ketan at ci.uchicago.edu Tue Nov 25 10:06:55 2014 From: ketan at ci.uchicago.edu (ketan at ci.uchicago.edu) Date: Tue, 25 Nov 2014 10:06:55 -0600 (CST) Subject: [Swift-commit] r8310 - SwiftApps/ematter Message-ID: <20141125160655.5E50D9D8B8@svn.ci.uchicago.edu> Author: ketan Date: 2014-11-25 10:06:54 -0600 (Tue, 25 Nov 2014) New Revision: 8310 Added: SwiftApps/ematter/runlocal Modified: SwiftApps/ematter/sites.local.xml SwiftApps/ematter/workflow.blues.swift Log: more comments in code Added: SwiftApps/ematter/runlocal =================================================================== --- SwiftApps/ematter/runlocal (rev 0) +++ SwiftApps/ematter/runlocal 2014-11-25 16:06:54 UTC (rev 8310) @@ -0,0 +1,3 @@ +#! /bin/sh + +/home/ketan/swift-0.95/cog/modules/swift/dist/swift-svn/bin/swift -sites.file sites.local.xml -config cf -tc.file apps workflow.blues.swift Property changes on: SwiftApps/ematter/runlocal ___________________________________________________________________ Added: svn:executable + * Modified: SwiftApps/ematter/sites.local.xml =================================================================== --- SwiftApps/ematter/sites.local.xml 2014-11-25 15:42:32 UTC (rev 8309) +++ SwiftApps/ematter/sites.local.xml 2014-11-25 16:06:54 UTC (rev 8310) @@ -1,4 +1,8 @@ + Modified: SwiftApps/ematter/workflow.blues.swift =================================================================== --- SwiftApps/ematter/workflow.blues.swift 2014-11-25 15:42:32 UTC (rev 8309) +++ SwiftApps/ematter/workflow.blues.swift 2014-11-25 16:06:54 UTC (rev 8310) @@ -68,9 +68,9 @@ } /* == Generate fdfs app definition == */ -app (file _fdf) gen_fdf(float _r, file _infdf) +app (file _fdf) gen_fdf(file _genfdf_src, float _r, file _infdf) { - genfdf _r @_infdf stdout=@_fdf; + bash @_genfdf_src _r @_infdf stdout=@_fdf; } /* == Smeagol transport Vn app definition == */ @@ -84,7 +84,7 @@ mpiexec "/home/heinonen/smeagol-1.2-Feb-2014/smeagol-1.2_blues/Src/smeagol-1.2_csg" stdin=@_inputfdf stdout=@_out; } -/* == Input files definitions == */ +/* == Input files definitions: Make sure these files are available in the current directory == */ file lammps_in <"in.lammps">; file lammps_geo <"AuTiO.geo">; file lammps_eam <"Au_u3.eam">; @@ -101,17 +101,17 @@ file pizza_src<"lastlammpsdump2xyz.py">; file pasta_src<"pasta">; +file genfdf_src<"genfdf">; - /* == Output files definitions == */ file xyz <"forsmeagol.xyz">; file lammps_dump <"lammps.dump">; file fdf_proc<"input_proc.fdf">; -file smeagol_lead_out <"out.smeagol.lead">; +file smeagol_lead_out <"smeagol_out/out.smeagol.lead">; +file smeagol_transport_out<"smeagol_out/out.smeagol_transport">; file au3dm <"Au3.DM">; file au3hst <"Au3.HST">; -file smeagol_transport_out<"out.smeagol_transport">; file bulklft <"bulklft.DAT">; file bulkrgt <"bulkrgt.DAT">; @@ -119,7 +119,7 @@ file tio2auhm<"TiO2Au.HM">; file tio2audm<"TiO2Au.DM">; -file[float] smeagol_transport_outn; file[float] fdf_proc_vn; @@ -132,6 +132,9 @@ /* == End files and variable declaration == */ + +/* == Invocation of apps == */ + /* == Invoke lammps == */ (lammps_dump) = lammps_app (lammps_in, lammps_geo, lammps_eam); @@ -166,7 +169,7 @@ foreach i in [Vstart:Vend:Vstep] { /* == generate fdfs for different voltages == */ -fdf_proc_vn[i]=gen_fdf(i,fdf_proc); +fdf_proc_vn[i]=gen_fdf(genfdf_src, i,fdf_proc); (smeagol_transport_outn[i]) = smeagol_vn_app(au3dm, au3hst, aupsf, ausicpsf, From ketan at ci.uchicago.edu Tue Nov 25 12:50:36 2014 From: ketan at ci.uchicago.edu (ketan at ci.uchicago.edu) Date: Tue, 25 Nov 2014 12:50:36 -0600 (CST) Subject: [Swift-commit] r8311 - SwiftApps/ematter Message-ID: <20141125185036.206769D8B8@svn.ci.uchicago.edu> Author: ketan Date: 2014-11-25 12:50:36 -0600 (Tue, 25 Nov 2014) New Revision: 8311 Modified: SwiftApps/ematter/apps SwiftApps/ematter/sites.local.xml Log: small change to sites Modified: SwiftApps/ematter/apps =================================================================== --- SwiftApps/ematter/apps 2014-11-25 16:06:54 UTC (rev 8310) +++ SwiftApps/ematter/apps 2014-11-25 18:50:36 UTC (rev 8311) @@ -16,4 +16,3 @@ localblues mpiexec mpiexec null null null localblues bash /bin/bash null null null localblues python /soft/python/2.7.6/bin/python null null null -localblues genfdf /home/ketan/ematter/smallrun/swift/genfdf null null null Modified: SwiftApps/ematter/sites.local.xml =================================================================== --- SwiftApps/ematter/sites.local.xml 2014-11-25 16:06:54 UTC (rev 8310) +++ SwiftApps/ematter/sites.local.xml 2014-11-25 18:50:36 UTC (rev 8311) @@ -9,7 +9,7 @@ 09:55:00 35000 36000 -/home/ketan/swiftwork +/tmp/swiftwork 0.09 From ketan at ci.uchicago.edu Tue Nov 25 17:58:38 2014 From: ketan at ci.uchicago.edu (ketan at ci.uchicago.edu) Date: Tue, 25 Nov 2014 17:58:38 -0600 (CST) Subject: [Swift-commit] r8312 - SwiftApps/ematter Message-ID: <20141125235838.52B879D8B8@svn.ci.uchicago.edu> Author: ketan Date: 2014-11-25 17:58:38 -0600 (Tue, 25 Nov 2014) New Revision: 8312 Added: SwiftApps/ematter/README Log: adding a README Added: SwiftApps/ematter/README =================================================================== --- SwiftApps/ematter/README (rev 0) +++ SwiftApps/ematter/README 2014-11-25 23:58:38 UTC (rev 8312) @@ -0,0 +1,2 @@ +README for the ematter Swift application. +More to come soon.