Merge pull request #110 from HECBioSim/issue108

Rest of the output directives added

longbow/schedulers/lsf.py

@@ -129,22 +129,22 @@ def prepare(job):
     jobfile.write("#BSUB -n " + job["cores"] + "\n")
 
     # Redirect stdout
-    if job["stdout"] == "":
+    if job["stdout"] != "":
 
-        jobfile.write("#BSUB -o %J.out")
+        jobfile.write("#BSUB -o " + job["stdout"] + "\n")
 
     else:
 
-        jobfile.write("#BSUB -o " + job["stdout"])
+        jobfile.write("#BSUB -o %J.out" + "\n")
 
     # Redirect stderr
-    if job["stderr"] == "":
+    if job["stderr"] != "":
 
-        jobfile.write("#BSUB -e %J.err")
+        jobfile.write("#BSUB -e " + job["stderr"] + "\n")
 
     else:
 
-        jobfile.write("#BSUB -e " + job["stderr"])
+        jobfile.write("#BSUB -e %J.err" + "\n")
 
     # Load any custom scripts.
     if job["scripts"] != "":

longbow/schedulers/pbs.py

@@ -160,6 +160,16 @@ def prepare(job):
         jobfile.write("#PBS -J 1-" + job["replicates"] + "\n")
         jobfile.write("#PBS -r y\n")
 
+    # Redirect stdout
+    if job["stdout"] != "":
+
+        jobfile.write("#PBS -o " + job["stdout"] + "\n")
+
+    # Redirect stderr
+    if job["stderr"] != "":
+
+        jobfile.write("#PBS -e " + job["stderr"] + "\n")
+
     # Set some environment variables for PBS.
     jobfile.write(
         "\n" + "export PBS_O_WORKDIR=$(readlink -f $PBS_O_WORKDIR)\n"

longbow/schedulers/sge.py

@@ -126,6 +126,16 @@ def prepare(job):
         jobfile.write("#$ -pe " + job["sge-peflag"] + " " +
                       job["cores"] + "\n\n")
 
+    # Redirect stdout
+    if job["stdout"] != "":
+
+        jobfile.write("#$ -o " + job["stdout"] + "\n")
+
+    # Redirect stderr
+    if job["stderr"] != "":
+
+        jobfile.write("#$ -e " + job["stderr"] + "\n\n")
+
     # Load any custom scripts.
     if job["scripts"] != "":
 

longbow/schedulers/slurm.py

@@ -137,6 +137,16 @@ def prepare(job):
     # Walltime for job
     jobfile.write("#SBATCH -t " + job["maxtime"] + ":00\n\n")
 
+    # Redirect stdout
+    if job["stdout"] != "":
+
+        jobfile.write("#SBATCH -o " + job["stdout"] + "\n")
+
+    # Redirect stderr
+    if job["stderr"] != "":
+
+        jobfile.write("#SBATCH -e " + job["stderr"] + "\n\n")
+
     # Load any custom scripts.
     if job["scripts"] != "":
 

longbow/schedulers/soge.py

@@ -150,6 +150,16 @@ def prepare(job):
 
     jobfile.write("#$ -pe ib " + cores + "\n\n")
 
+    # Redirect stdout
+    if job["stdout"] != "":
+
+        jobfile.write("#$ -o " + job["stdout"] + "\n")
+
+    # Redirect stderr
+    if job["stderr"] != "":
+
+        jobfile.write("#$ -e " + job["stderr"] + "\n\n")
+
     # Load any custom scripts.
     if job["scripts"] != "":
 

tests/standards/lsf_submitfiles/case1.txt

@@ -3,7 +3,9 @@
 #BSUB -q debug
 #BSUB -W 24:00
 #BSUB -n 24
+#BSUB -o %J.out
+#BSUB -e %J.err
 
 module load amber
 
-mpirun -lsf pmemd.MPI -O -i e.in -c e.min -p e.top -o e.out
+mpirun pmemd.MPI -O -i e.in -c e.min -p e.top -o e.out

tests/standards/lsf_submitfiles/case10.txt

@@ -0,0 +1,11 @@
+#!/bin/bash --login
+#BSUB -J testjob
+#BSUB -q debug
+#BSUB -W 24:00
+#BSUB -n 24
+#BSUB -o test.log
+#BSUB -e test.err
+
+module load amber
+
+mpirun pmemd.MPI -O -i e.in -c e.min -p e.top -o e.out

tests/standards/lsf_submitfiles/case2.txt

@@ -3,8 +3,10 @@
 #BSUB -q debug
 #BSUB -W 24:00
 #BSUB -n 24
+#BSUB -o %J.out
+#BSUB -e %J.err
 
 module load amber
 
 cd rep${LSB_JOBINDEX}/
-mpirun -lsf pmemd.MPI -O -i e.in -c e.min -p e.top -o e.out
+mpirun pmemd.MPI -O -i e.in -c e.min -p e.top -o e.out

tests/standards/lsf_submitfiles/case3.txt

@@ -4,7 +4,9 @@
 #BSUB -m cluster1
 #BSUB -W 24:00
 #BSUB -n 24
+#BSUB -o %J.out
+#BSUB -e %J.err
 
 module load amber
 
-mpirun -lsf pmemd.MPI -O -i e.in -c e.min -p e.top -o e.out
+mpirun pmemd.MPI -O -i e.in -c e.min -p e.top -o e.out

tests/standards/lsf_submitfiles/case4.txt

@@ -4,7 +4,9 @@
 #BSUB -P accno1234
 #BSUB -W 24:00
 #BSUB -n 24
+#BSUB -o %J.out
+#BSUB -e %J.err
 
 module load amber
 
-mpirun -lsf pmemd.MPI -O -i e.in -c e.min -p e.top -o e.out
+mpirun pmemd.MPI -O -i e.in -c e.min -p e.top -o e.out

tests/standards/lsf_submitfiles/case5.txt

@@ -4,7 +4,9 @@
 #BSUB -F accno1234
 #BSUB -W 24:00
 #BSUB -n 24
+#BSUB -o %J.out
+#BSUB -e %J.err
 
 module load amber
 
-mpirun -lsf pmemd.MPI -O -i e.in -c e.min -p e.top -o e.out
+mpirun pmemd.MPI -O -i e.in -c e.min -p e.top -o e.out

tests/standards/lsf_submitfiles/case6.txt

@@ -5,7 +5,9 @@
 #BSUB -u test.email@server.com
 #BSUB -W 24:00
 #BSUB -n 24
+#BSUB -o %J.out
+#BSUB -e %J.err
 
 module load amber
 
-mpirun -lsf pmemd.MPI -O -i e.in -c e.min -p e.top -o e.out
+mpirun pmemd.MPI -O -i e.in -c e.min -p e.top -o e.out

tests/standards/lsf_submitfiles/case7.txt

@@ -3,10 +3,12 @@
 #BSUB -q debug
 #BSUB -W 24:00
 #BSUB -n 24
+#BSUB -o %J.out
+#BSUB -e %J.err
 
 ls /dir
 cd /dir
 
 module load amber
 
-mpirun -lsf pmemd.MPI -O -i e.in -c e.min -p e.top -o e.out
+mpirun pmemd.MPI -O -i e.in -c e.min -p e.top -o e.out

tests/standards/lsf_submitfiles/case8.txt

@@ -3,6 +3,8 @@
 #BSUB -q debug
 #BSUB -W 24:00
 #BSUB -n 24
+#BSUB -o %J.out
+#BSUB -e %J.err
 
 module load amber
 

tests/standards/lsf_submitfiles/case9.txt

@@ -4,6 +4,8 @@
 #BSUB -R "rusage[mem=10G]"
 #BSUB -W 24:00
 #BSUB -n 24
+#BSUB -o %J.out
+#BSUB -e %J.err
 
 module load amber
 

tests/standards/pbs_submitfiles/case10.txt

@@ -0,0 +1,15 @@
+#!/bin/bash --login
+#PBS -N testjob
+#PBS -q debug
+#PBS -l select=1:ncpus=24:mpiprocs=24
+#PBS -l walltime=24:00:00
+#PBS -o test.log
+#PBS -e test.err
+
+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/sge_submitfiles/case9.txt

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

tests/standards/slurm_submitfiles/case9.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
+
+#SBATCH -o test.log
+#SBATCH -e test.err
+
+module load amber
+
+mpirun pmemd.MPI -O -i e.in -c e.min -p e.top -o e.out

tests/standards/soge_submitfiles/case9.txt

@@ -0,0 +1,14 @@
+#!/bin/bash --login
+#$ -cwd -V
+#$ -N testjob
+#$ -q debug
+#$ -l h_rt=24:00:00
+#$ -l nodes=1
+#$ -pe ib 24
+
+#$ -o test.log
+#$ -e test.err
+
+module load amber
+
+mpirun pmemd.MPI -O -i e.in -c e.min -p e.top -o e.out

tests/unit/schedulers_lsf/test_lsf_prepare.py

@@ -59,6 +59,8 @@ def test_prepare_case1():
         "modules": "amber",
         "queue": "debug",
         "replicates": "1",
+        "stdout": "",
+        "stderr": "",
         "scripts": "",
         "upload-include": "file1, file2"
     }
@@ -94,6 +96,8 @@ def test_prepare_case2():
         "modules": "amber",
         "queue": "debug",
         "replicates": "5",
+        "stdout": "",
+        "stderr": "",
         "scripts": "",
         "upload-include": "file1, file2"
     }
@@ -127,6 +131,8 @@ def test_prepare_case3():
         "modules": "amber",
         "queue": "debug",
         "replicates": "1",
+        "stdout": "",
+        "stderr": "",
         "scripts": "",
         "upload-include": "file1, file2"
     }
@@ -161,6 +167,8 @@ def test_prepare_case4():
         "modules": "amber",
         "queue": "debug",
         "replicates": "1",
+        "stdout": "",
+        "stderr": "",
         "scripts": "",
         "upload-include": "file1, file2"
     }
@@ -195,6 +203,8 @@ def test_prepare_case5():
         "modules": "amber",
         "queue": "debug",
         "replicates": "1",
+        "stdout": "",
+        "stderr": "",
         "scripts": "",
         "upload-include": "file1, file2"
     }
@@ -229,6 +239,8 @@ def test_prepare_case6():
         "modules": "amber",
         "queue": "debug",
         "replicates": "1",
+        "stdout": "",
+        "stderr": "",
         "scripts": "",
         "upload-include": "file1, file2"
     }
@@ -263,6 +275,8 @@ def test_prepare_case7():
         "modules": "amber",
         "queue": "debug",
         "replicates": "1",
+        "stdout": "",
+        "stderr": "",
         "scripts": "ls /dir, cd /dir",
         "upload-include": "file1, file2"
     }
@@ -297,6 +311,8 @@ def test_prepare_case8():
         "modules": "amber",
         "queue": "debug",
         "replicates": "1",
+        "stdout": "",
+        "stderr": "",
         "scripts": "",
         "upload-include": "file1, file2"
     }
@@ -331,6 +347,8 @@ def test_prepare_case9():
         "modules": "amber",
         "queue": "debug",
         "replicates": "1",
+        "stdout": "",
+        "stderr": "",
         "scripts": "",
         "upload-include": "file1, file2"
     }
@@ -341,3 +359,40 @@ def test_prepare_case9():
         os.path.join(
             os.getcwd(),
             "tests/standards/lsf_submitfiles/case9.txt"), "rb").read()
+
+
+def test_prepare_case10():
+
+    """
+    Stdout and stderr check
+    """
+
+    job = {
+        "account": "",
+        "cores": "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",
+        "lsf-cluster": "",
+        "maxtime": "24:00",
+        "memory": "",
+        "modules": "amber",
+        "queue": "debug",
+        "replicates": "1",
+        "stdout": "test.log",
+        "stderr": "test.err",
+        "scripts": "",
+        "upload-include": "file1, file2"
+    }
+
+    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/lsf_submitfiles/case10.txt"), "rb").read()