SGE tests for prepare method

Longbow/schedulers/sge.py

@@ -127,7 +127,9 @@ def prepare(job):
 
             for item in scripts:
 
-                jobfile.write(item.strip() + "\n\n")
+                jobfile.write(item.strip() + "\n")
+
+            jobfile.write("\n")
 
     # Add in module to be loaded.
     if job["modules"] is not "":

Tests/standards/sgesubfile_testcase1.txt

@@ -0,0 +1,10 @@
+#!/bin/bash --login
+#$ -cwd -V
+#$ -N testjob
+#$ -q debug
+#$ -l h_rt=24:00:00
+#$ -pe mpi 24
+
+module load amber
+
+mpirun -n 24 pmemd.MPI -O -i e.in -c e.min -p e.top -o e.out

Tests/standards/sgesubfile_testcase2.txt

@@ -0,0 +1,12 @@
+#!/bin/bash --login
+#$ -cwd -V
+#$ -N testjob
+#$ -q debug
+#$ -l h_rt=24:00:00
+#$ -t 1-5
+#$ -pe mpi 24
+
+module load amber
+
+cd rep${SGE_TASK_ID}/
+mpirun -n 24 pmemd.MPI -O -i e.in -c e.min -p e.top -o e.out

Tests/standards/sgesubfile_testcase3.txt

@@ -0,0 +1,11 @@
+#!/bin/bash --login
+#$ -cwd -V
+#$ -N testjob
+#$ -q debug
+#$ -A accno1234
+#$ -l h_rt=24:00:00
+#$ -pe mpi 24
+
+module load amber
+
+mpirun -n 24 pmemd.MPI -O -i e.in -c e.min -p e.top -o e.out

Tests/standards/sgesubfile_testcase4.txt

@@ -0,0 +1,11 @@
+#!/bin/bash --login
+#$ -cwd -V
+#$ -N testjob
+#$ -q debug
+#$ -P accno1234
+#$ -l h_rt=24:00:00
+#$ -pe mpi 24
+
+module load amber
+
+mpirun -n 24 pmemd.MPI -O -i e.in -c e.min -p e.top -o e.out

Tests/standards/sgesubfile_testcase5.txt

@@ -0,0 +1,12 @@
+#!/bin/bash --login
+#$ -cwd -V
+#$ -N testjob
+#$ -q debug
+#$ -l h_rt=24:00:00
+#$ -m bn
+#$ -M test.email@server.com
+#$ -pe mpi 24
+
+module load amber
+
+mpirun -n 24 pmemd.MPI -O -i e.in -c e.min -p e.top -o e.out

Tests/standards/sgesubfile_testcase6.txt

@@ -0,0 +1,13 @@
+#!/bin/bash --login
+#$ -cwd -V
+#$ -N testjob
+#$ -q debug
+#$ -l h_rt=24:00:00
+#$ -pe mpi 24
+
+ls /dir
+cd /dir
+
+module load amber
+
+mpirun -n 24 pmemd.MPI -O -i e.in -c e.min -p e.top -o e.out

Tests/standards/sgesubfile_testcase7.txt

@@ -0,0 +1,8 @@
+#!/bin/bash --login
+#$ -cwd -V
+#$ -N testjob
+#$ -q debug
+#$ -l h_rt=24:00:00
+module load amber
+
+mpiexec pmemd.MPI -O -i e.in -c e.min -p e.top -o e.out

Tests/unit/schedulers_sge/test_sge_prepare.py

@@ -22,17 +22,257 @@
 This test module contains tests for the SGE scheduler plugin.
 """
 
-try:
+import os
+import Longbow.schedulers.sge as sge
 
-    from unittest import mock
 
-except ImportError:
+def test_prepare_case1():
 
-    import mock
+    """
+    Simple test
+    """
 
-import pytest
+    job = {
+        "account": "",
+        "cluster": "",
+        "cores": "24",
+        "corespernode": "",
+        "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"
+    }
 
-import Longbow.corelibs.exceptions as exceptions
-import Longbow.schedulers.sge as sge
+    sge.prepare(job)
+
+    assert job["subfile"] == "submit.sge"
+    assert job["upload-include"] == "file1, file2, submit.sge"
+    assert open("/tmp/submit.sge", "rb").read() == open(
+        os.path.join(os.getcwd(),
+                     "Tests/standards/sgesubfile_testcase1.txt"), "rb").read()
+
+
+def test_prepare_case2():
+
+    """
+    Test replicates
+    """
+
+    job = {
+        "account": "",
+        "cluster": "",
+        "cores": "24",
+        "corespernode": "",
+        "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"
+    }
+
+    sge.prepare(job)
+
+    assert open("/tmp/submit.sge", "rb").read() == open(
+        os.path.join(os.getcwd(),
+                     "Tests/standards/sgesubfile_testcase2.txt"), "rb").read()
+
+
+def test_prepare_case3():
+
+    """
+    Test account parameter
+    """
+
+    job = {
+        "account": "accno1234",
+        "accountflag": "",
+        "cluster": "",
+        "cores": "24",
+        "corespernode": "",
+        "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"
+    }
+
+    sge.prepare(job)
+
+    assert open("/tmp/submit.sge", "rb").read() == open(
+        os.path.join(os.getcwd(),
+                     "Tests/standards/sgesubfile_testcase3.txt"), "rb").read()
+
+
+def test_prepare_case4():
+
+    """
+    Test account parameter
+    """
+
+    job = {
+        "account": "accno1234",
+        "accountflag": "-P",
+        "cluster": "",
+        "cores": "24",
+        "corespernode": "",
+        "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"
+    }
+
+    sge.prepare(job)
+
+    assert open("/tmp/submit.sge", "rb").read() == open(
+        os.path.join(os.getcwd(),
+                     "Tests/standards/sgesubfile_testcase4.txt"), "rb").read()
+
+
+def test_prepare_case5():
+
+    """
+    Test email parameters
+    """
+
+    job = {
+        "account": "",
+        "accountflag": "",
+        "cluster": "",
+        "cores": "24",
+        "corespernode": "",
+        "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"
+    }
+
+    sge.prepare(job)
+
+    assert open("/tmp/submit.sge", "rb").read() == open(
+        os.path.join(os.getcwd(),
+                     "Tests/standards/sgesubfile_testcase5.txt"), "rb").read()
+
+
+def test_prepare_case6():
+
+    """
+    Test script parameters
+    """
+
+    job = {
+        "account": "",
+        "accountflag": "",
+        "cluster": "",
+        "cores": "24",
+        "corespernode": "",
+        "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"
+    }
+
+    sge.prepare(job)
+
+    assert open("/tmp/submit.sge", "rb").read() == open(
+        os.path.join(os.getcwd(),
+                     "Tests/standards/sgesubfile_testcase6.txt"), "rb").read()
+
+
+def test_prepare_case7():
+
+    """
+    Test single core parameter for GPU
+    """
+
+    job = {
+        "account": "",
+        "accountflag": "",
+        "cluster": "",
+        "cores": "1",
+        "corespernode": "",
+        "executableargs": "pmemd.MPI -O -i e.in -c e.min -p e.top -o e.out",
+        "handler": "mpiexec",
+        "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"
+    }
 
+    sge.prepare(job)
 
+    assert open("/tmp/submit.sge", "rb").read() == open(
+        os.path.join(os.getcwd(),
+                     "Tests/standards/sgesubfile_testcase7.txt"), "rb").read()