Ordered GPUs according to PCI_BUS_ID in arbd/namd calls

atomicModel.py

@@ -1466,6 +1466,8 @@ if {$nLast == 0} {
         ## $bindir/charmrun +p$procs $bindir/namd2 +netpoll +idlepoll +devices $gpus $config &> $log
         gpus = ','.join([str(gpu) for gpu in gpus])
         # cmd = (charmrun, "+p%d" % numprocs, namd, '+netpoll',
+        env = os.environ.copy()
+        env["CUDA_DEVICE_ORDER"] = "PCI_BUS_ID"
         cmd = (namd,
                "+ppn", numprocs,
                '+netpoll','+idlepoll',
@@ -1476,4 +1478,4 @@ if {$nLast == 0} {
         logfile = "%s/%s.log" % (outputDirectory, outputPrefix)
         print("Running NAMD with: %s >& %s" % (" ".join(cmd), logfile) )
         with open(logfile,'w') as fh:
-            subprocess.call(cmd, stdout=fh, stderr=subprocess.STDOUT)
+            subprocess.call(cmd, env=env, stdout=fh, stderr=subprocess.STDOUT)

beadModel.py

@@ -315,6 +315,9 @@ class beadModel():
         self.writePsf( outputPrefix + ".psf" )
         self.writeArbdFiles( outputPrefix, numSteps=numSteps, timestep=timestep )
 
+        env = os.environ.copy()
+        env["CUDA_DEVICE_ORDER"] = "PCI_BUS_ID"
+
         ## http://stackoverflow.com/questions/18421757/live-output-from-subprocess-command
         # cmd = "%s -g %d %s.bd %s/%s" % (arbd, gpu, outputPrefix, outputDirectory, outputPrefix)
         # cmd = (arbd, (-g %d %s.bd %s/%s" % (gpu, outputPrefix, outputDirectory, outputPrefix))
@@ -322,7 +325,7 @@ class beadModel():
         cmd = tuple(str(x) for x in cmd)
 
         print("Running ARBD with: %s" % " ".join(cmd))
-        process = subprocess.Popen(cmd, stdout=subprocess.PIPE, universal_newlines=True)
+        process = subprocess.Popen(cmd, env=env, stdout=subprocess.PIPE, universal_newlines=True)
         for line in process.stdout:
         # for line in iter(process.stdout.readline, b''):
             sys.stdout.write(line)

beadModelTwist.py

@@ -384,6 +384,9 @@ class beadModelTwist():
         self.writePsf( outputPrefix + ".psf" )
         self.writeArbdFiles( outputPrefix, numSteps=numSteps, timestep=timestep )
 
+        env = os.environ.copy()
+        env["CUDA_DEVICE_ORDER"] = "PCI_BUS_ID"
+
         ## http://stackoverflow.com/questions/18421757/live-output-from-subprocess-command
         # cmd = "%s -g %d %s.bd %s/%s" % (arbd, gpu, outputPrefix, outputDirectory, outputPrefix)
         # cmd = (arbd, (-g %d %s.bd %s/%s" % (gpu, outputPrefix, outputDirectory, outputPrefix))
@@ -391,7 +394,7 @@ class beadModelTwist():
         cmd = tuple(str(x) for x in cmd)
 
         print("Running ARBD with: %s" % " ".join(cmd))
-        process = subprocess.Popen(cmd, stdout=subprocess.PIPE, universal_newlines=True)
+        process = subprocess.Popen(cmd, env=env, stdout=subprocess.PIPE, universal_newlines=True)
         for line in process.stdout:
         # for line in iter(process.stdout.readline, b''):
             sys.stdout.write(line)

run.py

@@ -52,6 +52,7 @@ def readAvgArbdCoords(psf,pdb,dcd,rmsdThreshold=3.5):
 
     # r0 = ref.xyz[0,ids,:]
     r0 = sel.xyz[-1,ids,:]
+    t = -1                      # in case dcd_frames < 3
     for t in range(len(sel.xyz)-2,-1,-1):
         # print(t)
         R,comA,comB = minimizeRmsd(sel.xyz[t,ids,:],r0)