[Swift-commit] r8421 - in SwiftApps: ematter subjobs
ketan at ci.uchicago.edu
ketan at ci.uchicago.edu
Tue Mar 31 19:01:18 CDT 2015
Author: ketan
Date: 2015-03-31 19:01:17 -0500 (Tue, 31 Mar 2015)
New Revision: 8421
Modified:
SwiftApps/ematter/workflow.bgq.swift
SwiftApps/subjobs/bg.sh
Log:
bgsh take care of preproc and postproc. ematter workflow args changes
Modified: SwiftApps/ematter/workflow.bgq.swift
===================================================================
--- SwiftApps/ematter/workflow.bgq.swift 2015-03-31 21:04:56 UTC (rev 8420)
+++ SwiftApps/ematter/workflow.bgq.swift 2015-04-01 00:01:17 UTC (rev 8421)
@@ -1,8 +1,7 @@
type file;
// Lammps app definition
-app (file _dump) lammps_app (string _lammps_exe, file _in,
- file _geo, file _eam)
+app (file _dump) lammps_app (string _lammps_exe, file _in, file _geo, file _eam, file _tinmeam, file _libmeam)
{
bgsh _lammps_exe "-in" @_in;
}
@@ -24,30 +23,15 @@
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 (string _smeagol_exe, file _aupsf,
- file _ausicpsf, file _inputfdf,
- file _opsf, file _osicpsf,
- file _tipsf, file _tisicpsf)
+app (file _tindm, file _tinhst, file _bulklft, file _bulkrgt, file _out) smeagol_lead_app (string _smeagol_exe, file _input_leadsfdf, file[] _psf)
{
- bgsh _smeagol_exe stdin=@_inputfdf stdout=@_out;
+ bgsh _smeagol_exe stdin=@_input_leadsfdf stdout=@_out;
}
-/* 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 ( 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 )
+app (file _out) smeagol_v0_app ( string _smeagol_exe, file _au3dm, file _au3hst,
+ file _bulklft, file _bulkrgt,
+ file _inputfdf, file[] _psf)
{
bgsh _smeagol_exe stdin=@_inputfdf stdout=@_out;
}
@@ -59,36 +43,29 @@
}
/* == 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 )
+app (file _trc_out, file _out) smeagol_vn_app (string _smeagol_exe, file _au3dm, file _au3hst, file _bulklft, file _bulkrgt, file _inputfdf, file[] _psf )
{
bgsh _smeagol_exe stdin=@_inputfdf stdout=@_out;
}
/* == Input files definitions: Make sure these files are available in the current directory == */
-file lammps_in <"input.lammps">;
-file lammps_geo <"AuTiO.geo">;
-file lammps_eam <"Au_u3.eam">;
+file lammps_in <"in.lammps">;
+file lammps_geo <"TiN-Ta-HfO2-TiN.geo">;
+file lammps_eam <"Ta.lammps.eam">;
+file tin_meam <"TiN.meam">;
+file lib_meam <"library.meam">;
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 psf[] <filesys_mapper; pattern="*.psf">;
file pizza_src<"lastlammpsdump2xyz.py">;
file pasta_src<"pasta">;
file genfdf_src<"genfdf">;
-string lammps_exe="/soft/applications/lammps/24Apr13/lmp_bgq_xlomp";
+//string lammps_exe="/soft/applications/lammps/24Apr13/lmp_bgq_xlomp";
+string lammps_exe="/home/knight/public/lammps/5Nov14/lmp_bgq_xlomp";
string smeagol_exe="/gpfs/mira-fs1/projects/Oxygen_defects_ALCC/share/bin/smeagol-1.2_csg";
@@ -100,8 +77,8 @@
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 tindm <"TiN.DM">;
+file tinhst <"TiN.HST">;
file bulklft <"bulklft.DAT">;
file bulkrgt <"bulkrgt.DAT">;
@@ -109,32 +86,23 @@
file tio2auhm<"TiO2Au.HM">;
file tio2audm<"TiO2Au.DM">;
-string Vs[]=["0.1","0.2","0.3","0.4","0.5","0.6","0.7","0.8","0.9","1.0"];
+string Vs[]=["0.1","0.2","0.3","0.4","0.5","0.6","0.7","0.8","0.9"];
//Invoke lammps
-(lammps_dump) = lammps_app (lammps_exe, lammps_in,
- lammps_geo, lammps_eam);
+(lammps_dump) = lammps_app (lammps_exe, lammps_in, lammps_geo, lammps_eam, tin_meam, lib_meam);
//Invoke smeagol lead
-(au3dm, au3hst,
+(tindm, tinhst,
bulklft, bulkrgt,
- smeagol_lead_out) = smeagol_lead_app (smeagol_exe, aupsf,
- ausicpsf, fdf_leads,
- opsf, osicpsf,
- tipsf, tisicpsf);
+ smeagol_lead_out) = smeagol_lead_app (smeagol_exe, fdf_leads, psf);
//Invoke pizza
(xyz) = pizza_app(pizza_src, lammps_dump);
//Invoke smeagol transport V0
-(tio2auhm, tio2audm,
- smeagol_transport_out) = smeagol_v0_app(smeagol_exe, au3dm,
- au3hst, aupsf, ausicpsf,
- bulklft, bulkrgt,
- fdf_v0, opsf, osicpsf,
- tipsf, tisicpsf);
+ (smeagol_transport_out) = smeagol_v0_app(smeagol_exe, tindm, tinhst, bulklft, bulkrgt, fdf_v0, psf);
//Invoke pasta
(fdf_proc) = pasta_app(pasta_src, xyz, fdf_v0);
@@ -152,10 +120,6 @@
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);
+(smeagol_trc_out, smeagol_transport_outn) = smeagol_vn_app(smeagol_exe, tindm, tinhst, bulklft, bulkrgt, fdf_proc_vn, psf);
-
}
Modified: SwiftApps/subjobs/bg.sh
===================================================================
--- SwiftApps/subjobs/bg.sh 2015-03-31 21:04:56 UTC (rev 8420)
+++ SwiftApps/subjobs/bg.sh 2015-04-01 00:01:17 UTC (rev 8421)
@@ -1,9 +1,15 @@
#!/bin/bash
-set -x
+#set -x
mname=$(hostname)
+#second arg is preprocess script
+preproc=$2
+
+#third arg is postproc script
+postproc=$3
+
# vesta and mira has different path than cetus
if [[ $mname == *vesta* || $mname == *mira* ]]
then
@@ -12,6 +18,9 @@
export PATH=/soft/cobalt/cetus/bgq_hardware_mapper:$PATH
fi
+#Run the preprocessing script
+./$preproc
+
#export SUBBLOCK_SIZE=16
# Prepare shape based on subblock size
@@ -97,5 +106,9 @@
echo "Finished Running in nonsubblock mode."
fi
+
+#Run the postprocessing script
+./$postproc
+
exit 0
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