Tests for PBS prepare

Longbow/schedulers/pbs.py

@@ -175,7 +175,9 @@ def prepare(job):
 
             for item in scripts:
 
-                jobfile.write(item.strip() + "\n\n")
+                jobfile.write(item.strip() + "\n")
+
+            jobfile.write("\n")
 
     # Load up modules if required.
     if job["modules"] is not "":

Tests/standards/pbssubfile_testcase1.txt

@@ -0,0 +1,13 @@
+#!/bin/bash --login
+#PBS -N testjob
+#PBS -q debug
+#PBS -l select=1:ncpus=24:mpiprocs=24
+#PBS -l walltime=24:00:00
+
+export PBS_O_WORKDIR=$(readlink -f $PBS_O_WORKDIR)
+cd $PBS_O_WORKDIR
+export OMP_NUM_THREADS=1
+
+module load amber
+
+mpirun pmemd.MPI -O -i e.in -c e.min -p e.top -o e.out

Tests/standards/pbssubfile_testcase2.txt

@@ -0,0 +1,18 @@
+#!/bin/bash --login
+#PBS -N testjob
+#PBS -q debug
+#PBS -l select=1:ncpus=24:mpiprocs=24
+#PBS -l walltime=24:00:00
+#PBS -J 1-5
+#PBS -r y
+
+export PBS_O_WORKDIR=$(readlink -f $PBS_O_WORKDIR)
+cd $PBS_O_WORKDIR
+export OMP_NUM_THREADS=1
+
+module load amber
+
+basedir=$PBS_O_WORKDIR 
+cd $basedir/rep${PBS_ARRAY_INDEX}/
+
+mpirun pmemd.MPI -O -i e.in -c e.min -p e.top -o e.out

Tests/standards/pbssubfile_testcase3.txt

@@ -0,0 +1,13 @@
+#!/bin/bash --login
+#PBS -N testjob
+#PBS -q debug
+#PBS -l select=1:ncpus=16:mpiprocs=16
+#PBS -l walltime=24:00:00
+
+export PBS_O_WORKDIR=$(readlink -f $PBS_O_WORKDIR)
+cd $PBS_O_WORKDIR
+export OMP_NUM_THREADS=1
+
+module load amber
+
+mpirun pmemd.MPI -O -i e.in -c e.min -p e.top -o e.out

Tests/standards/pbssubfile_testcase4.txt

@@ -0,0 +1,14 @@
+#!/bin/bash --login
+#PBS -N testjob
+#PBS -q debug
+#PBS -A accno1234
+#PBS -l select=1:ncpus=24:mpiprocs=24
+#PBS -l walltime=24:00:00
+
+export PBS_O_WORKDIR=$(readlink -f $PBS_O_WORKDIR)
+cd $PBS_O_WORKDIR
+export OMP_NUM_THREADS=1
+
+module load amber
+
+mpirun pmemd.MPI -O -i e.in -c e.min -p e.top -o e.out

Tests/standards/pbssubfile_testcase5.txt

@@ -0,0 +1,14 @@
+#!/bin/bash --login
+#PBS -N testjob
+#PBS -q debug
+#PBS -P accno1234
+#PBS -l select=1:ncpus=24:mpiprocs=24
+#PBS -l walltime=24:00:00
+
+export PBS_O_WORKDIR=$(readlink -f $PBS_O_WORKDIR)
+cd $PBS_O_WORKDIR
+export OMP_NUM_THREADS=1
+
+module load amber
+
+mpirun pmemd.MPI -O -i e.in -c e.min -p e.top -o e.out

Tests/standards/pbssubfile_testcase6.txt

@@ -0,0 +1,15 @@
+#!/bin/bash --login
+#PBS -N testjob
+#PBS -q debug
+#PBS -l select=1:ncpus=24:mpiprocs=24
+#PBS -m bn
+#PBS -M test.email@server.com
+#PBS -l walltime=24:00:00
+
+export PBS_O_WORKDIR=$(readlink -f $PBS_O_WORKDIR)
+cd $PBS_O_WORKDIR
+export OMP_NUM_THREADS=1
+
+module load amber
+
+mpirun pmemd.MPI -O -i e.in -c e.min -p e.top -o e.out

Tests/standards/pbssubfile_testcase7.txt

@@ -0,0 +1,16 @@
+#!/bin/bash --login
+#PBS -N testjob
+#PBS -q debug
+#PBS -l select=1:ncpus=24:mpiprocs=24
+#PBS -l walltime=24:00:00
+
+export PBS_O_WORKDIR=$(readlink -f $PBS_O_WORKDIR)
+cd $PBS_O_WORKDIR
+export OMP_NUM_THREADS=1
+
+ls /dir
+cd /dir
+
+module load amber
+
+mpirun pmemd.MPI -O -i e.in -c e.min -p e.top -o e.out

Tests/standards/pbssubfile_testcase8.txt

@@ -0,0 +1,13 @@
+#!/bin/bash --login
+#PBS -N testjob
+#PBS -q debug
+#PBS -l select=1:ncpus=24:mpiprocs=24
+#PBS -l walltime=24:00:00
+
+export PBS_O_WORKDIR=$(readlink -f $PBS_O_WORKDIR)
+cd $PBS_O_WORKDIR
+export OMP_NUM_THREADS=1
+
+module load amber
+
+aprun -n 24 -N 24 pmemd.MPI -O -i e.in -c e.min -p e.top -o e.out

Tests/standards/pbssubfile_testcase9.txt

@@ -0,0 +1,13 @@
+#!/bin/bash --login
+#PBS -N testjob
+#PBS -q debug
+#PBS -l select=1:ncpus=24:mpiprocs=24:mem=8gb
+#PBS -l walltime=24:00:00
+
+export PBS_O_WORKDIR=$(readlink -f $PBS_O_WORKDIR)
+cd $PBS_O_WORKDIR
+export OMP_NUM_THREADS=1
+
+module load amber
+
+aprun -n 24 -N 24 pmemd.MPI -O -i e.in -c e.min -p e.top -o e.out

Tests/unit/schedulers_lsf/test_lsf_prepare.py

@@ -85,8 +85,6 @@ def test_prepare_case2():
 
     lsf.prepare(job)
 
-    assert job["subfile"] == "submit.lsf"
-    assert job["upload-include"] == "file1, file2, submit.lsf"
     assert open("/tmp/submit.lsf", "rb").read() == open(
         os.path.join(os.getcwd(),
                      "Tests/standards/lsfsubfile_testcase2.txt"), "rb").read()
@@ -118,8 +116,6 @@ def test_prepare_case3():
 
     lsf.prepare(job)
 
-    assert job["subfile"] == "submit.lsf"
-    assert job["upload-include"] == "file1, file2, submit.lsf"
     assert open("/tmp/submit.lsf", "rb").read() == open(
         os.path.join(os.getcwd(),
                      "Tests/standards/lsfsubfile_testcase3.txt"), "rb").read()
@@ -152,8 +148,6 @@ def test_prepare_case4():
 
     lsf.prepare(job)
 
-    assert job["subfile"] == "submit.lsf"
-    assert job["upload-include"] == "file1, file2, submit.lsf"
     assert open("/tmp/submit.lsf", "rb").read() == open(
         os.path.join(os.getcwd(),
                      "Tests/standards/lsfsubfile_testcase4.txt"), "rb").read()
@@ -186,8 +180,6 @@ def test_prepare_case5():
 
     lsf.prepare(job)
 
-    assert job["subfile"] == "submit.lsf"
-    assert job["upload-include"] == "file1, file2, submit.lsf"
     assert open("/tmp/submit.lsf", "rb").read() == open(
         os.path.join(os.getcwd(),
                      "Tests/standards/lsfsubfile_testcase5.txt"), "rb").read()
@@ -220,8 +212,6 @@ def test_prepare_case6():
 
     lsf.prepare(job)
 
-    assert job["subfile"] == "submit.lsf"
-    assert job["upload-include"] == "file1, file2, submit.lsf"
     assert open("/tmp/submit.lsf", "rb").read() == open(
         os.path.join(os.getcwd(),
                      "Tests/standards/lsfsubfile_testcase6.txt"), "rb").read()
@@ -230,7 +220,7 @@ def test_prepare_case6():
 def test_prepare_case7():
 
     """
-    Test email parameters
+    Test script parameters
     """
 
     job = {
@@ -254,8 +244,6 @@ def test_prepare_case7():
 
     lsf.prepare(job)
 
-    assert job["subfile"] == "submit.lsf"
-    assert job["upload-include"] == "file1, file2, submit.lsf"
     assert open("/tmp/submit.lsf", "rb").read() == open(
         os.path.join(os.getcwd(),
                      "Tests/standards/lsfsubfile_testcase7.txt"), "rb").read()
@@ -264,7 +252,7 @@ def test_prepare_case7():
 def test_prepare_case8():
 
     """
-    Test email parameters
+    Test handler parameters
     """
 
     job = {
@@ -288,8 +276,6 @@ def test_prepare_case8():
 
     lsf.prepare(job)
 
-    assert job["subfile"] == "submit.lsf"
-    assert job["upload-include"] == "file1, file2, submit.lsf"
     assert open("/tmp/submit.lsf", "rb").read() == open(
         os.path.join(os.getcwd(),
                      "Tests/standards/lsfsubfile_testcase8.txt"), "rb").read()