[Swift-commit] r8318 - SwiftApps/ematter
ketan at ci.uchicago.edu
ketan at ci.uchicago.edu
Wed Dec 3 15:55:57 CST 2014
Author: ketan
Date: 2014-12-03 15:55:57 -0600 (Wed, 03 Dec 2014)
New Revision: 8318
Modified:
SwiftApps/ematter/runbgq
SwiftApps/ematter/sites.cobalt-local.xml
SwiftApps/ematter/workflow.bgq.swift
Log:
worker logging off
Modified: SwiftApps/ematter/runbgq
===================================================================
--- SwiftApps/ematter/runbgq 2014-12-03 01:57:42 UTC (rev 8317)
+++ SwiftApps/ematter/runbgq 2014-12-03 21:55:57 UTC (rev 8318)
@@ -1,4 +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/ketan/swift-0.95/cog/modules/swift/dist/swift-svn/bin/swift -sites.file sites.cobalt-local.xml -config cf -tc.file apps workflow.bgq.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
Modified: SwiftApps/ematter/sites.cobalt-local.xml
===================================================================
--- SwiftApps/ematter/sites.cobalt-local.xml 2014-12-03 01:57:42 UTC (rev 8317)
+++ SwiftApps/ematter/sites.cobalt-local.xml 2014-12-03 21:55:57 UTC (rev 8318)
@@ -16,12 +16,16 @@
<profile namespace="globus" key="maxnodes">32</profile>
<profile namespace="globus" key="nodegranularity">32</profile>
<profile key="SUBBLOCK_SIZE" namespace="env">8</profile>
-<profile key="WORKER_LOGGING_LEVEL" namespace="env">DEBUG</profile>
+
+<!--
+<profile key="WORKER_LOGGING_LEVEL" namespace="env">NONE</profile>
<profile key="ENABLE_WORKER_LOGGING" namespace="env">TRUE</profile>
<profile key="ENABLE_WORKER_LOGGING" namespace="env">ON</profile>
<profile key="WORKER_LOG_DIR" namespace="env">/home/ketan/workerlogs</profile>
<profile namespace="globus" key="workerLoggingLevel">DEBUG</profile>
<profile namespace="globus" key="workerLoggingDirectory">/home/ketan/workerlogs</profile>
+-->
+
<profile namespace="globus" key="jobsPerNode">4</profile>
<workdirectory>/home/ketan/swiftwork</workdirectory>
Modified: SwiftApps/ematter/workflow.bgq.swift
===================================================================
--- SwiftApps/ematter/workflow.bgq.swift 2014-12-03 01:57:42 UTC (rev 8317)
+++ SwiftApps/ematter/workflow.bgq.swift 2014-12-03 21:55:57 UTC (rev 8318)
@@ -1,23 +1,22 @@
type file;
// Lammps app definition
-app (file _dump, file _out,
- file _err) lammps_app (string _lammps_exe, file _in,
+app (file _dump) lammps_app (string _lammps_exe, file _in,
file _geo, file _eam)
{
- bgsh _lammps_exe "-in" @_in stdout=@_out stderr=@_err;
+ bgsh _lammps_exe "-in" @_in;
}
// Pizza app definition
-app (file _xyz, file _out, file _err) pizza_app (file _pizza_src, file _dump)
+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
-app (file _fdf, file _out, file _err) pasta_app (file _pasta_src, file _xyz, file _fdf_tmp)
+app (file _fdf) pasta_app (file _pasta_src, file _xyz, file _fdf_tmp)
{
- bash @_pasta_src @_xyz @_fdf_tmp @_fdf stdout=@_out stderr=@_err;
+ bash @_pasta_src @_xyz @_fdf_tmp @_fdf;
}
/* smeagol lead inputs
@@ -27,12 +26,12 @@
//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 _out) 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;
+ bgsh _smeagol_exe stdin=@_inputfdf stdout=@_out;
}
/* smeagol transport V0 inputs
@@ -43,89 +42,119 @@
//Smeagol transport V0 app definition
app (file _tio2auhm, file _tio2audm,
- file _out, file _err) smeagol_v0_app ( string _smeagol_exe, file _au3dm,
+ file _out) 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;
+ bgsh _smeagol_exe stdin=@_inputfdf stdout=@_out;
}
-//Smeagol transport Vn app definition
-//app () smeagol_vn_app (){}
+/* == Generate fdfs app definition == */
+app (file _fdf) gen_fdf(file _genfdf_src, float _r, file _infdf)
+{
+ bash @_genfdf_src _r @_infdf stdout=@_fdf;
+}
-// Files
+/* == Smeagol transport Vn app definition == */
+app (file _trc_out, file _out) smeagol_vn_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;
+}
+
+/* == 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">;
-file lammps_out <"out.lammps">;
-file lammps_err <"err.lammps">;
-file lammps_dump <"lammps.dump">;
+file fdf_leads<"input_leads.fdf">;
+file fdf_v0<"input_t0.fdf">;
-string lammps_exe="/soft/applications/lammps/24Apr13/lmp_bgq_xlomp";
+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 lammps
-(lammps_dump, lammps_out, lammps_err) = lammps_app (lammps_exe, lammps_in,
- lammps_geo, lammps_eam);
-
file pizza_src<"lastlammpsdump2xyz.py">;
+file pasta_src<"pasta">;
+file genfdf_src<"genfdf">;
-file pizza_out <"out.pizza">;
-file pizza_err <"err.pizza">;
-file xyz <"forsmeagol.xyz">;
+string lammps_exe="/soft/applications/lammps/24Apr13/lmp_bgq_xlomp";
+string smeagol_exe="/gpfs/mira-fs1/projects/Oxygen_defects_ALCC/share/bin/smeagol-1.2_csg";
-//Invoke pizza
-(xyz, pizza_out, pizza_err) = pizza_app(pizza_src, lammps_dump);
-file fdf_in<"input_leads.fdf">;
+/* == Output files definitions == */
+file xyz <"forsmeagol.xyz">;
+file lammps_dump <"lammps.dump">;
+file fdf_proc<"input_proc.fdf">;
-file pasta_src<"pasta">;
-
-file smeagol_lead_out <"out.smeagol.lead">;
-file smeagol_lead_err <"err.smeagol.lead">;
+file smeagol_lead_out <"smeagol_out/smeagol.lead.out">;
+file smeagol_transport_out<"smeagol_out/smeagol.transport.out">;
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 tio2auhm<"TiO2Au.HM">;
+file tio2audm<"TiO2Au.DM">;
-string smeagol_exe="/gpfs/mira-fs1/projects/Oxygen_defects_ALCC/share/bin/smeagol-1.2_csg";
+string Vs[]=["0.1","0.2","0.3","0.4","0.5","0.6","0.7","0.8","0.9","1.0"];
+//Invoke lammps
+(lammps_dump) = lammps_app (lammps_exe, 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_err) = smeagol_lead_app (smeagol_exe, aupsf,
- ausicpsf, fdf_in,
+ smeagol_lead_out) = smeagol_lead_app (smeagol_exe, aupsf,
+ ausicpsf, fdf_leads,
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);
+ smeagol_transport_out) = smeagol_v0_app(smeagol_exe, au3dm,
+ au3hst, aupsf, ausicpsf,
+ bulklft, bulkrgt,
+ fdf_v0, opsf, osicpsf,
+ tipsf, tisicpsf);
+//Invoke pasta
+(fdf_proc) = pasta_app(pasta_src, xyz, fdf_v0);
+
+foreach v,i in Vs
+{
+/* == generate fdfs for different voltages == */
+string fdfname = strcat("input_", v, ".fdf");
+file fdf_proc_vn <single_file_mapper; file=fdfname>;
+
+fdf_proc_vn = gen_fdf(genfdf_src, toFloat(v), fdf_proc);
+
+string outname = strcat("smeagol_out/bias_", v, ".out");
+file smeagol_transport_outn <single_file_mapper; file=outname>;
+
+file smeagol_trc_out <single_file_mapper; file=strcat("0.TiO2Au_", v, ".TRC")>;
+
+(smeagol_trc_out, smeagol_transport_outn) = smeagol_vn_app(smeagol_exe, au3dm, au3hst,
+ aupsf, ausicpsf, bulklft, bulkrgt,
+ fdf_proc_vn, opsf, osicpsf, tipsf,
+ tisicpsf);
+
+
+}
+
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