scripts and info for /export/apps

src/nbcr-nfs/Makefile

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+REDHAT.ROOT = $(CURDIR)/../../
+
+-include $(ROCKSROOT)/etc/Rules.mk
+include Rules.mk
+
+build:
+
+install::
+	mkdir -p -m 755 $(ROOT)/$(PKGROOT)/bin
+	install -m 755 bin/*  $(ROOT)/$(PKGROOT)/bin
+	mkdir -p -m 755 $(ROOT)/$(PKGROOT)/info
+	install -m 644 info/*  $(ROOT)/$(PKGROOT)/info
+
+clean::

src/nbcr-nfs/bin/showVisGpu

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+#!/opt/python/bin/python2.7
+
+import os
+import sys
+import subprocess
+from pprint import pprint
+
+class GPUinfo:
+    """ base class """
+    def __init__(self, argv):
+        self.usage_command = os.path.basename(argv[0])
+        self.args          = argv[1:]
+        self.space         = '    '
+        self.specinfo      = ''
+        self.nameinfo      = 'checks for available GPU ids'
+        self.descinfo      = 'outputs free GPU ids as a comma-separated string\n' + \
+                             '%sNUM - number of GPUs to use for a job' % self.space
+        self.cmd           = '/usr/bin/nvidia-smi'
+        self.utilization   = 7  # utilization field in nvidia-smi output (without "| /" characters)
+        self.numgpu        = 1
+        self.numgpuMax     = 8   # max gpu count on a node
+        self.freeids       = []  # list of free gpus
+        self.env           = 'CUDA_VISIBLE_DEVICES'  # environ variable to set 
+
+        self.parseArgs()
+
+    def parseArgs(self):
+        """ check input arguments, and print usage"""
+        if len(self.args) == 0:
+            return
+        if self.args[0] in ('-h', '--help', 'help'):
+            self.help()
+        # first argument is number of desired gpus
+        numgpu = int(self.args[0])
+        if numgpu > 8 :
+            numgpu = 8
+        self.numgpu = numgpu
+
+    def help(self):
+        print "\nNAME\n%s%s - %s." % (self.space, self.usage_command, self.nameinfo)
+        print '\nSYNOPSIS\n', self.space + self.usage_command, "NUM", "[-h|--help|help]"
+        print '\nDESCRIPTION\n', self.space +  self.descinfo
+        print self.specinfo
+        sys.exit(0)
+
+    def runTest(self):
+        """ test output """
+        pprint (self.__dict__)
+
+    def nvsmi(self):
+        """find output of nvidia-smi"""
+        __name__ = "nvsmi"
+
+        cmd = "%s | grep %%" % self.cmd
+        info, err = subprocess.Popen(cmd, shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE).communicate()
+        if err: 
+            print "%s returned error: %s" % (self.cmd,err)
+
+        info = info.translate(None, "|/") # remove | and /
+        lines = info.split('\n')[:-1]  # split into lines, rm last new line
+
+        return lines
+
+    def findFree(self, lines):
+        """ find list of free GPU ids from a given output"""
+        for i in range (len(lines)):
+            parts = lines[i].split()
+            util = int(parts[self.utilization][:-1])
+            if util < 1:
+                self.freeids.append(i)
+        return 
+
+    def setVisible(self):
+        strVis = str(self.freeids[0:self.numgpu]).strip('[]')
+        strVis = strVis.replace(' ','')
+        print  strVis
+
+        #os.environ[self.env] = a
+
+    def run(self):
+        lines = self.nvsmi()  # run nvidia-smi command
+        self.findFree(lines)  # find free gpu ids
+        self.setVisible()
+
+### Main ###
+app = GPUinfo(sys.argv)
+app.run()

src/nbcr-nfs/bin/startVNC

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+#!/bin/bash
+
+acc=`whoami`
+port=${acc:4:2}
+
+if [ "$acc" == "npw" ]; then
+    port=25
+fi
+if [ "$acc" == "yin" ]; then
+    port=26
+fi
+
+echo "Using display :$port for vnc"
+rocks run host compute-0-1 command="vncserver :$port"
+

src/nbcr-nfs/bin/stopVNC

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+#!/bin/bash
+
+acc=`whoami`
+port=${acc:4:2}
+
+if [ "$acc" == "npw" ]; then
+    port=25
+fi
+if [ "$acc" == "yin" ]; then
+    port=26
+fi
+
+rocks run host compute-0-1 command="vncserver -kill :$port"
+

src/nbcr-nfs/info/amber.sub

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+#!/bin/bash
+#$ -V
+#$ -e amber-suit.e 
+#$ -o amber-suit.o 
+#$ -cwd
+#$ -S /bin/bash
+#$ -q gpu
+#$ -l gpu=4
+#$ -pe orte 4
+
+# this example reqeusts 4 cpus and 4 gpus
+# the required switches are above last 3 lines
+
+# load the needed enviornment
+module load amber14/gnu
+
+# WORKAROUND to find free GPUs
+# note number in the line below equals number of GPUs used in -l gpu line above
+export CUDA_VISIBLE_DEVICES=`/share/apps/bin/showVisGpu 4`
+
+# run your amber commands (cd to directory with input files)
+cd $HOME/amber-run1 
+$AMBERHOME/bin/pmemd.cuda -O -i mdin.GPU -o mdout.1GPU -inf mdinfo.1GPU -x mdcrd.1GPU -r restrt.1GPU
+

src/nbcr-nfs/info/amberGaMD.sub

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+#!/bin/bash
+#$ -V
+#$ -e amber-suit.e 
+#$ -o amber-suit.o 
+#$ -cwd
+#$ -S /bin/bash
+#$ -q gpu
+#$ -l gpu=1
+#$ -pe orte 4
+
+# this example reqeusts 4 cpus and 1 gpu
+# the request for GPU queue, number of CPUs, and number of GPUs are above last 3 lines
+
+# load the needed enviornment
+module load amberGaMD14/gnu
+
+# WORKAROUND to find free GPUs
+# note number in the line below equals number of GPUs used in -l gpu line above
+export CUDA_VISIBLE_DEVICES=`/share/apps/bin/showVisGpu 1`
+
+# run your amber commands (cd to directory with input files)
+# YOURACCOUNT is your login name
+cd /data/YOURACCOUNT/amber-run1 
+$AMBERHOME/bin/pmemd.cuda -O -i mdin.GPU -o mdout.1GPU -inf mdinfo.1GPU -x mdcrd.1GPU -r restrt.1GPU
+

src/nbcr-nfs/info/modules

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+
+All applicaitons environment is set using modules.
+From the list of available modules load modules needed by your application.
+
+In general, modules that require other modules load them as a prerequisite
+so that no extra loading will be implicitely needed. Applications modules 
+loading must be done in SGE submit script or on a command line.
+
+To list available modules :
+    module avail
+
+To load needed modules:
+    Example 1. load for amber14 compiled with gnu compiler:
+        module load amber14/gnu  
+
+    Example 2. load for matlab
+        module load matlab
+
+To list loaded modules:
+        module list
+
+To unload a module:
+        module unload matlab
+
+Unloading is only needed if switching  for differently compiled versions of the same application
+or if the previously loaded moduules conflict with a  new needed.
+
+For more info run: 
+        man module
+

src/nbcr-nfs/version.mk

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+NAME       = nbcr-nfs
+VERSION    = 1
+RELEASE    = 0
+PKGROOT    = /export/apps/