Tests for slurm prepare method

Longbow/schedulers/slurm.py

@@ -133,7 +133,9 @@ 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/slurmsubfile_testcase1.txt

@@ -0,0 +1,10 @@
+#!/bin/bash --login
+#SBATCH -J testjob
+#SBATCH -p debug
+#SBATCH -n 24
+#SBATCH -N 1
+#SBATCH -t 24:00:00
+
+module load amber
+
+mpirun pmemd.MPI -O -i e.in -c e.min -p e.top -o e.out

Tests/standards/slurmsubfile_testcase2.txt

@@ -0,0 +1,16 @@
+#!/bin/bash --login
+#SBATCH -J testjob
+#SBATCH -p debug
+#SBATCH -n 24
+#SBATCH -N 1
+#SBATCH -t 24:00:00
+
+module load amber
+
+basedir = `pwd`
+for i in {1..5};
+do
+  cd $basedir/rep$i/
+  mpirun pmemd.MPI -O -i e.in -c e.min -p e.top -o e.out
+done
+wait

Tests/standards/slurmsubfile_testcase3.txt

@@ -0,0 +1,11 @@
+#!/bin/bash --login
+#SBATCH -J testjob
+#SBATCH -p debug
+#SBATCH -A accno1234
+#SBATCH -n 24
+#SBATCH -N 1
+#SBATCH -t 24:00:00
+
+module load amber
+
+mpirun pmemd.MPI -O -i e.in -c e.min -p e.top -o e.out

Tests/standards/slurmsubfile_testcase4.txt

@@ -0,0 +1,11 @@
+#!/bin/bash --login
+#SBATCH -J testjob
+#SBATCH -p debug
+#SBATCH -P accno1234
+#SBATCH -n 24
+#SBATCH -N 1
+#SBATCH -t 24:00:00
+
+module load amber
+
+mpirun pmemd.MPI -O -i e.in -c e.min -p e.top -o e.out

Tests/standards/slurmsubfile_testcase5.txt

@@ -0,0 +1,12 @@
+#!/bin/bash --login
+#SBATCH -J testjob
+#SBATCH -p debug
+#SBATCH --mail-type=bn
+#SBATCH --mail-user=test.email@server.com
+#SBATCH -n 24
+#SBATCH -N 1
+#SBATCH -t 24:00:00
+
+module load amber
+
+mpirun pmemd.MPI -O -i e.in -c e.min -p e.top -o e.out

Tests/standards/slurmsubfile_testcase6.txt

@@ -0,0 +1,13 @@
+#!/bin/bash --login
+#SBATCH -J testjob
+#SBATCH -p debug
+#SBATCH -n 24
+#SBATCH -N 1
+#SBATCH -t 24:00:00
+
+ls /dir
+cd /dir
+
+module load amber
+
+mpirun pmemd.MPI -O -i e.in -c e.min -p e.top -o e.out

Tests/unit/schedulers_slurm/test_slurm_prepare.py

@@ -26,3 +26,223 @@
 import Longbow.schedulers.slurm as slurm
 
 
+def test_prepare_case1():
+
+    """
+    Simple test
+    """
+
+    job = {
+        "account": "",
+        "cluster": "",
+        "cores": "24",
+        "corespernode": "24",
+        "executableargs": "pmemd.MPI -O -i e.in -c e.min -p e.top -o e.out",
+        "handler": "mpirun",
+        "email-address": "",
+        "email-flags": "",
+        "jobname": "testjob",
+        "localworkdir": "/tmp",
+        "maxtime": "24:00",
+        "memory": "",
+        "modules": "amber",
+        "queue": "debug",
+        "replicates": "1",
+        "scripts": "",
+        "sge-peflag": "mpi",
+        "sge-peoverride": "false",
+        "upload-include": "file1, file2"
+    }
+
+    slurm.prepare(job)
+
+    assert job["subfile"] == "submit.slurm"
+    assert job["upload-include"] == "file1, file2, submit.slurm"
+    assert open("/tmp/submit.slurm", "rb").read() == open(
+        os.path.join(
+            os.getcwd(),
+            "Tests/standards/slurmsubfile_testcase1.txt"), "rb").read()
+
+
+def test_prepare_case2():
+
+    """
+    Test replicates
+    """
+
+    job = {
+        "account": "",
+        "cluster": "",
+        "cores": "24",
+        "corespernode": "24",
+        "executableargs": "pmemd.MPI -O -i e.in -c e.min -p e.top -o e.out",
+        "handler": "mpirun",
+        "email-address": "",
+        "email-flags": "",
+        "jobname": "testjob",
+        "localworkdir": "/tmp",
+        "maxtime": "24:00",
+        "memory": "",
+        "modules": "amber",
+        "queue": "debug",
+        "replicates": "5",
+        "scripts": "",
+        "sge-peflag": "mpi",
+        "sge-peoverride": "false",
+        "upload-include": "file1, file2"
+    }
+
+    slurm.prepare(job)
+
+    assert open("/tmp/submit.slurm", "rb").read() == open(
+        os.path.join(
+            os.getcwd(),
+            "Tests/standards/slurmsubfile_testcase2.txt"), "rb").read()
+
+
+def test_prepare_case3():
+
+    """
+    Test account parameter
+    """
+
+    job = {
+        "account": "accno1234",
+        "accountflag": "",
+        "cluster": "",
+        "cores": "24",
+        "corespernode": "24",
+        "executableargs": "pmemd.MPI -O -i e.in -c e.min -p e.top -o e.out",
+        "handler": "mpirun",
+        "email-address": "",
+        "email-flags": "",
+        "jobname": "testjob",
+        "localworkdir": "/tmp",
+        "maxtime": "24:00",
+        "memory": "",
+        "modules": "amber",
+        "queue": "debug",
+        "replicates": "1",
+        "scripts": "",
+        "sge-peflag": "mpi",
+        "sge-peoverride": "false",
+        "upload-include": "file1, file2"
+    }
+
+    slurm.prepare(job)
+
+    assert open("/tmp/submit.slurm", "rb").read() == open(
+        os.path.join(
+            os.getcwd(),
+            "Tests/standards/slurmsubfile_testcase3.txt"), "rb").read()
+
+
+def test_prepare_case4():
+
+    """
+    Test account parameter
+    """
+
+    job = {
+        "account": "accno1234",
+        "accountflag": "-P",
+        "cluster": "",
+        "cores": "24",
+        "corespernode": "24",
+        "executableargs": "pmemd.MPI -O -i e.in -c e.min -p e.top -o e.out",
+        "handler": "mpirun",
+        "email-address": "",
+        "email-flags": "",
+        "jobname": "testjob",
+        "localworkdir": "/tmp",
+        "maxtime": "24:00",
+        "memory": "",
+        "modules": "amber",
+        "queue": "debug",
+        "replicates": "1",
+        "scripts": "",
+        "sge-peflag": "mpi",
+        "sge-peoverride": "false",
+        "upload-include": "file1, file2"
+    }
+
+    slurm.prepare(job)
+
+    assert open("/tmp/submit.slurm", "rb").read() == open(
+        os.path.join(
+            os.getcwd(),
+            "Tests/standards/slurmsubfile_testcase4.txt"), "rb").read()
+
+
+def test_prepare_case5():
+
+    """
+    Test email parameters
+    """
+
+    job = {
+        "account": "",
+        "accountflag": "",
+        "cluster": "",
+        "cores": "24",
+        "corespernode": "24",
+        "executableargs": "pmemd.MPI -O -i e.in -c e.min -p e.top -o e.out",
+        "handler": "mpirun",
+        "email-address": "test.email@server.com",
+        "email-flags": "bn",
+        "jobname": "testjob",
+        "localworkdir": "/tmp",
+        "maxtime": "24:00",
+        "memory": "",
+        "modules": "amber",
+        "queue": "debug",
+        "replicates": "1",
+        "scripts": "",
+        "sge-peflag": "mpi",
+        "sge-peoverride": "false",
+        "upload-include": "file1, file2"
+    }
+
+    slurm.prepare(job)
+
+    assert open("/tmp/submit.slurm", "rb").read() == open(
+        os.path.join(
+            os.getcwd(),
+            "Tests/standards/slurmsubfile_testcase5.txt"), "rb").read()
+
+
+def test_prepare_case6():
+
+    """
+    Test script parameters
+    """
+
+    job = {
+        "account": "",
+        "accountflag": "",
+        "cluster": "",
+        "cores": "24",
+        "corespernode": "24",
+        "executableargs": "pmemd.MPI -O -i e.in -c e.min -p e.top -o e.out",
+        "handler": "mpirun",
+        "email-address": "",
+        "email-flags": "",
+        "jobname": "testjob",
+        "localworkdir": "/tmp",
+        "maxtime": "24:00",
+        "memory": "",
+        "modules": "amber",
+        "queue": "debug",
+        "replicates": "1",
+        "scripts": "ls /dir, cd /dir",
+        "sge-peflag": "mpi",
+        "sge-peoverride": "false",
+        "upload-include": "file1, file2"
+    }
+
+    slurm.prepare(job)
+
+    assert open("/tmp/submit.slurm", "rb").read() == open(
+        os.path.join(
+            os.getcwd(),
+            "Tests/standards/slurmsubfile_testcase6.txt"), "rb").read()