Merge pull request #54 from bio-phys/fix-filename

Fix filename bug

Author: kain88-de

changelog/54.bugfix

@@ -0,0 +1 @@
+Fixed edge-case in input filename parsing.

mdbenchmark/generate.py

@@ -113,9 +113,8 @@ def generate(name, gpu, module, host, min_nodes, max_nodes, time, list_hosts):
             directory += '_gpu'
             gpu_string = ' with GPUs'
 
-        # Check and append the correct extensions for a given module.
-        # If not files exist as expected, we stop here.
-        engine_input = engine.check_file_extension(name)
+        # Check if all needed files exist. Throw an error if they do not.
+        engine.check_input_file_exists(name)
 
         console.info('Creating benchmark system for {}.', m + gpu_string)
         number_of_benchmarks = (len(module) * (max_nodes + 1 - min_nodes))
@@ -126,8 +125,15 @@ def generate(name, gpu, module, host, min_nodes, max_nodes, time, list_hosts):
 
         top = dtr.Tree(directory)
         for n in range(min_nodes, max_nodes + 1):
-            engine.write_bench(top, tmpl, n, gpu, m, engine_input, name, host,
-                               time)
+            engine.write_bench(
+                top=top,
+                tmpl=tmpl,
+                nodes=n,
+                gpu=gpu,
+                module=m,
+                name=name,
+                host=host,
+                time=time)
 
     # Provide some output for the user
     console.info('Finished generating all benchmarks.\n'

mdbenchmark/mdengines/gromacs.py

@@ -105,8 +105,8 @@ def analyze_run(sim):
             sim.categories['gpu'], sim.categories['host'], ncores)
 
 
-def write_bench(top, tmpl, nodes, gpu, module, tpr, name, host, time):
-    """ Writes a single gromacs benchmark file and the respective sim object
+def write_bench(top, tmpl, nodes, gpu, module, name, host, time):
+    """Generates a single job file for GROMACS and the respective Sim object.
     """
     sim = mds.Sim(
         top['{}/'.format(nodes)],
@@ -120,7 +120,12 @@ def write_bench(top, tmpl, nodes, gpu, module, tpr, name, host, time):
             'started': False
         })
 
-    copyfile(tpr, sim[tpr].relpath)
+    full_filename = name + '.tpr'
+    if name.endswith('.tpr'):
+        full_filename = name
+        name = name[:-4]
+
+    copyfile(full_filename, sim[full_filename].relpath)
     # Add some time buffer to the requested time. Otherwise the queuing system
     # kills the jobs before GROMACS can finish
     formatted_time = '{:02d}:{:02d}:00'.format(*divmod(time + 5, 60))
@@ -140,22 +145,20 @@ def write_bench(top, tmpl, nodes, gpu, module, tpr, name, host, time):
         fh.write(script)
 
 
-def check_file_extension(name):
-    """ check and append the correct file extensions for the given module.
+def check_input_file_exists(name):
+    """Check if the TPR file exists.
     """
-    # Check that the .tpr file exists.
-    fn, ext = os.path.splitext(name)
-
-    if ext == '':
-        ext = '.tpr'
+    fn = name
+    if fn.endswith('.tpr'):
+        fn = name[:-4]
 
-    tpr = fn + ext
+    tpr = fn + '.tpr'
     if not os.path.exists(tpr):
         console.error(
             "File {} does not exist, but is needed for GROMACS benchmarks.",
             tpr)
 
-    return tpr
+    return
 
 
 def cleanup_before_restart(sim):

mdbenchmark/mdengines/namd.py

@@ -94,9 +94,13 @@ def analyze_run(sim):
             sim.categories['host'], ncores)
 
 
-def write_bench(top, tmpl, nodes, gpu, module, tpr, name, host, time):
+def write_bench(top, tmpl, nodes, gpu, module, name, host, time):
     """ Writes a single namd benchmark file and the respective sim object
     """
+    # Strip the file extension, if we were given one.
+    # This makes the usage of `mdbenchmark generate` equivalent between NAMD and GROMACS.
+    if name.endswith('.namd'):
+        name = name[:-5]
     sim = mds.Sim(
         top['{}/'.format(nodes)],
         categories={
@@ -162,18 +166,21 @@ def analyze_namd_file(fh):
             console.error('No absolute path detected in NAMD file!')
 
 
-def check_file_extension(name):
+def check_input_file_exists(name):
     """Check and append the correct file extensions for the NAMD module.
     """
     # Check whether the needed files are there.
     for extension in ['namd', 'psf', 'pdb']:
+        if name.endswith('.{}'.format(extension)):
+            name = name[:-1 + len(extension)]
+
         fn = '{}.{}'.format(name, extension)
         if not os.path.exists(fn):
             console.error(
                 "File {} does not exist, but is needed for NAMD benchmarks.",
                 fn)
 
-    return name
+    return
 
 
 def cleanup_before_restart(sim):

mdbenchmark/tests/mdengines/test_gromacs.py

@@ -118,7 +118,7 @@ def test_cli():
 
     @test_cli.command()
     def test():
-        gromacs.check_file_extension('md')
+        gromacs.check_input_file_exists('md')
 
     output = 'ERROR File md.tpr does not exist, but is needed for GROMACS benchmarks.\n'
     result = cli_runner.invoke(test_cli, ['test'])

mdbenchmark/tests/mdengines/test_namd.py

@@ -79,7 +79,7 @@ def test_cli():
 
     @test_cli.command()
     def test():
-        namd.check_file_extension('md')
+        namd.check_input_file_exists('md')
 
     output = 'ERROR File md.namd does not exist, but is needed for NAMD benchmarks.\n'
     result = cli_runner.invoke(test_cli, ['test'])

mdbenchmark/tests/test_generate.py

@@ -20,7 +20,6 @@
 import os
 
 import pytest
-
 from mdbenchmark import cli
 from mdbenchmark.ext.click_test import cli_runner
 
@@ -72,6 +71,14 @@ def test_generate(cli_runner, tmpdir, tpr_file):
             assert os.path.exists(
                 'draco_gromacs/2016_gpu/{}/bench.job'.format(i))
 
+        # Make sure we pass the correct file name to the job template. It
+        # should not contain any file extensions for GROMACS.
+        with open('draco_gromacs/2016_gpu/6/bench.job') as f:
+            for line in f:
+                if not line.startswith('srun'):
+                    continue
+                assert line.endswith('-deffnm protein')
+
 
 def test_generate_console_messages(cli_runner, tmpdir):
     """Test that the CLI for generate prints all error messages as expected."""