Refs #1 appeding runs in Titan

confinedBSA.ipynb

@@ -1,7 +1,7 @@
 {
  "metadata": {
   "name": "",
-  "signature": "sha256:ef7345964cc06b385cc7928593141d314816b906ac38ec526f8c5b4e6c052ab0"
+  "signature": "sha256:7efccddce4926f586126358e699b2fb57192002e42928bc6941c7d22a455cecf"
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  "nbformat": 3,
  "nbformat_minor": 0,
@@ -528,7 +528,20 @@
       "gmx mdrun -ntmpi 16 -ntomp 1 -pin on -deffnm equil_1\n",
       "</code>\n",
       "\n",
-      "<center><a href=\"files/simulation/silica/cristobalite/confineBSA/poretop/yesbonds/wholesystem/minimize.gif\"><img src=\"files/simulation/silica/cristobalite/confineBSA/poretop/yesbonds/wholesystem/minimize.gif\" width=\"250\"></a>  [minimize.vmd](files/simulation/silica/cristobalite/confineBSA/poretop/yesbonds/onlysilica/minimize.vmd) </center>  "
+      "<center><a href=\"files/simulation/silica/cristobalite/confineBSA/poretop/yesbonds/wholesystem/minimize.gif\"><img src=\"files/simulation/silica/cristobalite/confineBSA/poretop/yesbonds/wholesystem/minimize.gif\" width=\"250\"></a>  [minimize.vmd](files/simulation/silica/cristobalite/confineBSA/poretop/yesbonds/onlysilica/minimize.vmd) </center>  \n",
+      "\n",
+      "The 2ns relaxation at NPT (<code>relax_2</code>) proved insufficiently long since the pressure became negative in the <code>equil_1</code> run. Thus, we extend the simulation for 10ns in Titan by appending 1ns jobs. For this we need to transfer to Titan all files <code>relax_2.*</code> and the following  \n",
+      "\n",
+      "- create soft link <code>ln -s relax_2.tpr relax_2.0.tpr</code>\n",
+      "- template submission script [relax_2.extend.tpl](files/simulation/silica/cristobalite/confineBSA/poretop/yesbonds/wholesystem/relax_2.extend.tpl)\n",
+      "- substitution script: [relax_2.submitnext.sh](files/simulation/silica/cristobalite/confineBSA/poretop/yesbonds/wholesystem/relax_2.submitnext.sh)\n",
+      "\n",
+      "In Titan, we just run the substitution script by passing as argument the number of the firs run:  \n",
+      "<code>./relax_2.submitnext.sh 0</code>  \n",
+      "Will trigger submission of the first nanosecond, followed by 9 more runs up to a total of 10ns\n",
+      "\n",
+      "\n",
+      "\n"
      ]
     },
     {

simulation/silica/cristobalite/confineBSA/poretop/yesbonds/wholesystem/relax_2.extend.tpl

@@ -0,0 +1,33 @@
+#!/bin/bash
+#PBS -q batch
+#PBS -A MAT049
+#PBS -N q0.90_ovl1.5
+#PBS -j oe
+#PBS -l nodes=4
+#PBS -l walltime=02:00:00
+#PBS -l gres=atlas1%atlas2
+
+export CRAY_CUDA_MPS=1
+source $MODULESHOME/init/bash
+module load gromacs/5.1.0
+
+# iteration control
+extratime=1000   # extend simulations by this much (in picoseconds)
+last=10  # no more than these simulations
+prev=_PREV_
+curr=$(($prev + 1))
+
+cd $PBS_O_WORKDIR
+# Extend the run
+aprun -n 1 gmx_mpi convert-tpr -s relax_2.${prev}.tpr -extend $extratime -o relax_2.${curr}.tpr
+# 8 MPI ranks per node, each one tied to 2 openMP threads
+aprun -n 32 -N 8 -d 2 gmx_mpi mdrun -ntomp 2 -gpu_id 00000000 -s relax_2.${curr}.tpr -cpi relax_2.cpt -deffnm relax_2 -append
+
+# submit next job
+if [ $curr -eq $last ];
+then
+  echo "last simulation done"
+  exit
+fi
+./relax_2.submitnext.sh $curr  # submit next job
+

simulation/silica/cristobalite/confineBSA/poretop/yesbonds/wholesystem/relax_2.submitnext.sh

@@ -0,0 +1,9 @@
+#!/bin/bash
+if [ -z "$1" ];
+then
+  echo "need to pass a number as argument"
+  exit 1
+fi
+sed -e "s/_PREV_/$1/g" relax_2.extend.tpl > relax_2.extend.pbs
+qsub relax_2.extend.pbs
+