Print --report-bindings to stderr

vitduck · Mar 26, 2022 · b85a2b4 · b85a2b4
1 parent e2fa6d5
commit b85a2b4
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Showing 3 changed files with 23 additions and 22 deletions.
diff --git a/src/env.py b/src/env.py
@@ -5,7 +5,8 @@
 import subprocess
 
 def module_list():
-    logging.info(f'{"Modules":<7} : {" ".join(os.environ["LOADEDMODULES"].split(os.pathsep))}')
+    if 'LOADEDMODULES' in os.environ:
+        logging.info(f'{"Modules":<7} : {" ".join(os.environ["LOADEDMODULES"].split(os.pathsep))}')
 
 def module_purge():
     cmd = subprocess.run(['modulecmd', 'python', 'purge'], stdout=subprocess.PIPE).stdout.decode('utf-8')

diff --git a/src/gromacs.py b/src/gromacs.py
@@ -42,7 +42,7 @@ def __init__(self, input='stmv.tpr', nsteps=10000, resetstep=0, nstlist=0, pin='
 
         self.src       = ['http://ftp.gromacs.org/pub/gromacs/gromacs-2021.3.tar.gz']
 
-        self.header    = ['input', 'node', 'task', 'omp', 'gpu', 'perf(ns/day)', 'time(s)']
+        self.header    = ['input', 'node', 'task', 'omp', 'gpu', 'nstlist', 'perf(ns/day)', 'time(s)']
 
         # cmdline option
         self.parser.usage        = '%(prog)s -i stmv.tpr --nsteps 4000'
@@ -102,7 +102,8 @@ def run(self):
            f'{os.path.splitext(os.path.basename(self.input))[0]}-'
                f'n{self.mpi.node}-'
                f't{self.mpi.task}-' 
-               f'o{self.mpi.omp}.log' )
+               f'o{self.mpi.omp}-'
+               f'l{self.nstlist}.log' )
 
         if self.mpi.gpu:
             self.output = re.sub(r'(-o\d+)', rf'\1-g{self.mpi.gpu}', self.output, 1)
@@ -119,7 +120,7 @@ def run(self):
             os.remove('ener.edr')
 
     def parse(self):
-        key = ",".join(map(str, [self.mpi.node, self.mpi.task, self.mpi.omp, self.gpu]))
+        key = ",".join(map(str, [self.mpi.node, self.mpi.task, self.mpi.omp, self.gpu, self.nstlist]))
 
         with open(self.output, 'r') as fh:
             for line in fh:
@@ -161,7 +162,7 @@ def mdrun(self):
     def parse(self):
         key = ",".join(map(str, [
             os.path.basename(self.input), 
-            self.mpi.node, self.mpi.task, self.mpi.omp, self.mpi.gpu ]))
+            self.mpi.node, self.mpi.task, self.mpi.omp, self.mpi.gpu, self.nstlist ]))
 
         with open('md.log', 'r') as fh:
             for line in fh:

diff --git a/src/utils.py b/src/utils.py
@@ -23,23 +23,22 @@ def sync(nodelist=[]):
 def syscmd(cmd, output=None):
     logging.debug(cmd)
 
-    pout = '' 
+    pipe = subprocess.run(cmd, shell=True, text=True, capture_output=True)
 
-    try: 
-        pout = subprocess.check_output(cmd, stderr=subprocess.STDOUT, shell=True).decode('utf-8').rstrip()
-    except subprocess.CalledProcessError as e:
-        # Work around required for QE/6.8
-        # https://forums.developer.nvidia.com/t/unusual-behavior/136392/2
-        if e.returncode == 2:
-            if output:
-                with open(output, "w") as output_fh:
-                    output_fh.write(f'{e.stdout.decode("utf-8").rstrip()}')
-        else:
-            logging.error(f'{e.stderr.decode("utf-8").rstrip()}')
-            sys.exit()
-    else: 
-        if output: 
+    # Work around required for QE/6.8
+    # https://forums.developer.nvidia.com/t/unusual-behavior/136392/2
+    if pipe.returncode == 0 or pipe.returncode == 2:
+        if output:
             with open(output, "w") as output_fh:
-                output_fh.write(pout)
+                # openmpi  --report-bindings
+                if pipe.stderr: 
+                    for line in pipe.stderr.splitlines():
+                        if re.search('^\[.+?\] MCW', line): 
+                            logging.error(line)
+
+                output_fh.write(pipe.stdout)
         else: 
-            return pout
+            return pipe.stdout
+    else: 
+        logging.error(pipe.stderr)
+        sys.exit()