Building Git 2.6.3 from source, I ran into this error:
    DB2TEXI user-manual.texi
/bin/sh: line 1: docbook2x-texi: command not found
This is the docbook to texi converter from the docbook2X package (which has not been updated since 2007).

For Red Hat and Fedora, the EPEL package repo provides docbook2X. However, the name of the script is changed because there is a newer docbook package. So, in the git source directory, edit the file Documentation/Makefile and change one line:

DOCBOOK2X_TEXI = db2x_docbook2texi


SWIG is great - Python DRMAA2 interface in less than an hour

I have never used SWIG before, surprisingly. I figured creating a Python interface to DRMAA2 would be a good self-tutorial. Turns out to be almost trivial, following the directions here.

My Python (3.5) DRMAA2 interface code is on GitHub - https://github.com/prehensilecode/pydrmaa2. The hardest part, really, was writing the Makefile.

NOTE: no testing at all has been done. This is just a Q&D exercise to use SWIG.


Autotools mythbuster

This is a really useful site by Diego Elio “Flameeyes” Pettenò that clarifies and provides good examples of autotools usage: https://autotools.io/index.html


Modernized makefiles for VASP 5.3

One of the research groups on the cluster I manage requested help in compiling VASP 5.3 (the Vienna Ab-intitio Simulation Package), code for electronic structure calculations and QM molecular dynamics from first principles. Like many research codes, the build procedure is a bit difficult owing to legacy stuff.

I updated the makefiles for my build, to more current GNU Make standards. They worked for me; however, I make no guarantee that they will work for you. In fact, they will likely not work for you without modification. In any case, the repo is on GitHub. Fork away!



Apache Spark integration with Grid Engine

Apache Spark is a fast engine for big data. It can use Hadoop infrastructure (like HDFS), and provides its own map-reduce implementation. It can also be run in standalone mode, without Hadoop or the YARN resource manager.

I have been able to get Spark 1.4.1 running, with some integration into an existing Univa Grid Engine cluster. The integration is not "tight" in that the slave processes are still independently launched with ssh. I was unable to get Spark to work with qrsh. So, without tight integration, usage accounting is not exact.

I also had to make some modifications to the Spark standalone shell scripts in order to have job-specific configuration and log directories. Out of the box, Spark's shell scripts do not completely propagate the environment to the slaves. Job-specific configuration and log directories are needed because multiple users may want to run Spark jobs at the same time.

Additionally, I was not able to figure a way to constrain Spark slave instances to subsets of available processor cores. So, Spark jobs require exclusive use of compute nodes.

So, let's start there. Your GE installation needs to have the "exclusive" complex defined:

#name               shortcut   type        relop   requestable consumable default  urgency 
exclusive           excl       BOOL        EXCL    YES         YES        0        1000

The OS on Drexel's Proteus cluster is RHEL 6.4-ish. I use Red Hat's packaging of Oracle Java 1.7.0_85 by default. Running Spark requires the JAVA_HOME environment variable to be set, which I do in the global login script location /etc/profile.d/. I found that using /usr/lib/jvm/java did not work. It needed to be:


Building Spark 1.4.1 was painless. I used the bundled script to generate a binary distribution tarball:

     ./make-distribution.sh --name myname --tgz

Untar it into some convenient location. 

Next, the sbin/start-slaves.sh and sbin/stop-slaves.sh scripts need to be modified. You can look at my fork at GitHub. As they are, these two scripts just ssh to all the slave nodes to start the slave processes. However, ssh does not pass environment variables, so all the slave processes launch with the default SPARK_HOME. That means all the slave processes read the global Spark config and environment, and log to the global Spark installation log directory.

Because the remote shell is the user shell, we have to figure out the user shell in order to build the command to be executed on the slave hosts. Here is the snippet from sbin/start-slaves.sh:

# Launch the slaves
USERSHELL=$( getent passwd $USER | cut -f7 -d: )
if [ $USERSHELL = "/bin/bash" -o $USERSHELL = "/bin/zsh" -o $USERSHELL = "/bin/ksh" ] ; then
    "$sbin/slaves.sh" cd "$SPARK_HOME" \&\& "." "$SPARK_CONF_DIR/spark-env.sh" \&\& "$sbin/start-slave.sh" "spark://$SPARK_MASTER_IP:$SPARK_MASTER_PORT"
elif [ $USERSHELL = "/bin/tcsh" -o $USERSHELL = "/bin/csh" ] ; then
    "$sbin/slaves.sh" cd "$SPARK_HOME" \&\& "source" "$SPARK_CONF_DIR/spark-env.csh" \&\& "$sbin/start-slave.sh" "spark://$SPARK_MASTER_IP:$SPARK_MASTER_PORT"

The cluster here has two types of compute nodes: Dell C6145s with 64-core AMD CPUs, and Dell C6220s with 16-core Intel CPUs. So, I created a job class (JC) with two subclasses, and also separate parallel environments (PEs).

The job class is as follows -- all missing lines have the default "{+}UNSPECIFIED" config:

jcname          spark
variant_list    default intel amd
owner           NONE
user_lists      NONE
xuser_lists     NONE
l_hard          {+}exclusive=TRUE,h_vmem=4g,m_mem_free=3g, \
                [{+}intel=vendor=intel,h_vmem=4g,m_mem_free=3g], \
pe_name         {~}spark.intel,[intel=spark.intel],[amd=spark.amd]

The spark.intel PE is defined as follows (with the spark.amd PE defined similarly):

pe_name                spark.intel
slots                  99999
user_lists             NONE
xuser_lists            NONE
start_proc_args        /cm/shared/apps/sge/var/default/common/pescripts/sparkstart.sh
stop_proc_args         NONE
allocation_rule        16
control_slaves         FALSE
job_is_first_task      FALSE
urgency_slots          min
accounting_summary     FALSE
daemon_forks_slaves    FALSE
master_forks_slaves    FALSE

The PE start script writes the job-specific environment files, and log4j properties file:


/bin/mkdir -p ${spark_conf_dir}

### for bash-like

echo "#!/usr/bin/env bash" > $sparkenvfile
echo "export JAVA_HOME=/usr/lib/jvm/java-1.7.0-oracle.x86_64" >> $sparkenvfile
echo "export SPARK_CONF_DIR=${spark_conf_dir}" >> $sparkenvfile
echo "export SPARK_MASTER_WEBUI_PORT=8880" >> $sparkenvfile
echo "export SPARK_WORKER_WEBUI_PORT=8881" >> $sparkenvfile
echo "export SPARK_WORKER_INSTANCES=1" >> $sparkenvfile

spark_master_ip=$( cat ${PE_HOSTFILE} | head -1 | cut -f1 -d\  )
echo "export SPARK_MASTER_IP=${spark_master_ip}" >> $sparkenvfile

echo "export SPARK_MASTER_PORT=7077" >> $sparkenvfile
echo "export MASTER_URL=spark://${spark_master_ip}:7077" >> $sparkenvfile

echo "export SPARK_SLAVES=${spark_slaves}" >> $sparkenvfile

spark_worker_cores=$( expr ${NSLOTS} / ${NHOSTS} )
echo "export SPARK_WORKER_CORES=${spark_worker_cores}" >> $sparkenvfile

echo "export SPARK_WORKER_DIR=${spark_worker_dir}" >> $sparkenvfile

echo "export SPARK_LOG_DIR=${spark_log_dir}" >> $sparkenvfile

echo "export SPARK_LOCAL_DIRS=${TMP}" >> $sparkenvfile

chmod +x $sparkenvfile

### for csh-like

echo "#!/usr/bin/env tcsh" > $sparkenvfile
echo "setenv JAVA_HOME /usr/lib/jvm/java-1.7.0-oracle.x86_64" >> $sparkenvfile
echo "setenv SPARK_CONF_DIR ${spark_conf_dir}" >> $sparkenvfile
echo "setenv SPARK_MASTER_WEBUI_PORT 8880" >> $sparkenvfile
echo "setenv SPARK_WORKER_WEBUI_PORT 8881" >> $sparkenvfile
echo "setenv SPARK_WORKER_INSTANCES 1" >> $sparkenvfile

spark_master_ip=$( cat ${PE_HOSTFILE} | head -1 | cut -f1 -d\  )
echo "setenv SPARK_MASTER_IP ${spark_master_ip}" >> $sparkenvfile

echo "setenv SPARK_MASTER_PORT 7077" >> $sparkenvfile
echo "setenv MASTER_URL spark://${spark_master_ip}:7077" >> $sparkenvfile

echo "setenv SPARK_SLAVES ${spark_slaves}" >> $sparkenvfile

spark_worker_cores=$( expr ${NSLOTS} / ${NHOSTS} )
echo "setenv SPARK_WORKER_CORES ${spark_worker_cores}" >> $sparkenvfile

echo "setenv SPARK_WORKER_DIR ${spark_worker_dir}" >> $sparkenvfile

echo "setenv SPARK_LOG_DIR ${spark_log_dir}" >> $sparkenvfile

echo "setenv SPARK_LOCAL_DIRS ${TMP}" >> $sparkenvfile

chmod +x $sparkenvfile

/bin/mkdir -p ${spark_log_dir}
/bin/mkdir -p ${spark_worker_dir}
cat ${PE_HOSTFILE} | cut -f1 -d \  > ${spark_slaves}

### defaults, sp. log directory
echo "spark.eventLog.dir    ${spark_log_dir}" > ${spark_conf_dir}/spark-defaults.conf

### log4j defaults
echo "### Suggestion: use "WARN" or "ERROR"; use "INFO" when debugging" > $log4j_props
echo "# Set everything to be logged to the console" >> $log4j_props
echo "log4j.rootCategory=WARN, console" >> $log4j_props
echo "log4j.appender.console=org.apache.log4j.ConsoleAppender" >> $log4j_props
echo "log4j.appender.console.target=System.err" >> $log4j_props
echo "log4j.appender.console.layout=org.apache.log4j.PatternLayout" >> $log4j_props
echo "log4j.appender.console.layout.ConversionPattern=%d{yy/MM/dd HH:mm:ss} %p %c{1}: %m%n" >> $log4j_props
echo "# Settings to quiet third party logs that are too verbose" >> $log4j_props
echo "log4j.logger.org.spark-project.jetty=WARN" >> $log4j_props
echo "log4j.logger.org.spark-project.jetty.util.component.AbstractLifeCycle=ERROR" >> $log4j_props
echo "log4j.logger.org.apache.spark.repl.SparkIMain$exprTyper=INFO" >> $log4j_props
echo "log4j.logger.org.apache.spark.repl.SparkILoop$SparkILoopInterpreter=INFO" >> $log4j_props

And then an example job script looks like:

#$ -S /bin/bash
#$ -P myprj
#$ -M myemail@example.com
#$ -m ea
#$ -j y
#$ -cwd
#$ -jc spark.intel
#$ -l exclusive
#$ -pe spark.intel 32
#$ -l vendor=intel
#$ -l h_rt=0:30:00
#$ -l h_vmem=4g
#$ -l m_mem_free=3g
. /etc/profile.d/modules.sh
module load shared
module load proteus
module load gcc
module load sge/univa
module load python/2.7-current
module load apache/spark/1.4.1
### Set up environment for Spark
. ${SPARK_CONF_DIR}/spark-env.sh
### The actual work is done below
### Start the cluster: master first, then slaves
echo "Starting master on ${SPARK_MASTER_IP} ..."
echo "Done starting master."
echo "Starting slave..."
echo "Done starting slave."
### the script which does the actual computation is submitted to the 
### standalone Spark cluster
echo "Submitting job..."
spark-submit --master $MASTER_URL wordcount.py
echo "Done job."
### Stop the cluster: slaves first, then master
echo "Stopping slaves..."
echo "Done stopping slaves"
echo "Stopping master..."
echo "Done stopping master."

And, that's it. I have not done extensive testing or benchmarking, so I don't know what the performance is like relative to an installation that runs on Hadoop with HDFS. 


Abaqus integration for Univa Grid Engine (update)

My last post about Abaqus integration with Univa Grid Engine (UGE) had one disadvantage: it did not use qrsh to launch the slave MPI processes. As a result, job resource usage accounting was inaccurate. To fix this, certain parallel environment (PE) settings need to be corrected, and the rsh command that Abaqus uses for launching MPI slaves needs to be set to the wrapper rsh script.

The PE settings which worked worked for me -- see also sge_pe(5)

pe_name                abaqus
slots                  99999
user_lists             NONE
xuser_lists            NONE
start_proc_args        /cm/shared/apps/sge/var/default/common/pescripts/abaqus.py
stop_proc_args         NONE
allocation_rule        $round_robin
control_slaves         TRUE
job_is_first_task      FALSE
urgency_slots          min
accounting_summary     TRUE
daemon_forks_slaves    TRUEmaster_forks_slaves    FALSE

And the updated PE script (again, setting the mp_host_list is optional). The rsh command is actually the rsh wrapper shell script, which then calls qrsh.

#!/usr/bin/env python
import sys, os

### PE startup script aka prologue to set up Abaqus MPI "hostfile"
### Based on documented env file format
###     http://www.simulia.com/support/v67/books/sgb67EF/default.htm?startat=ch04s01.html

machinefile = os.environ['PE_HOSTFILE']
abaqenvfile = "abaqus_v6.env"

machinelines = []
with open(machinefile, "ro") as mf:
    for l in mf:
        lsplit = l.split()
        machinelines.append( [lsplit[0], int(lsplit[1])] )

with open(abaqenvfile, "wo") as envfile:
    envfile.write("mp_rsh_command='/cm/shared/apps/sge/univa/mpi/rsh -n -l %U %H %C'\n")
    envfile.write("mp_host_list=%s\n" % (str(machinelines)))


Jupyter (FKA iPython) project gets $6m funding

The Helmsley Charitable Trust, the Alfred P. Sloan Foundation, and the Gordon and Betty Moore Foundation just announced a $6m grant to UC Berkeley and Cal Poly to fund Project Jupyter. Jupyter evolved from the iPython project, abstracting the language-agnostic parts. It also serves as an interactive shell for Python 3, Julia, R, Haskell, and Ruby. I think the most notable thing it provides is a web-based GUI “notebook” similar to what has been available in Maple and Mathematica for a while. (Maybe Matlab, too: I have not used Matlab much.)

Correction: Jupyter serves as an interactive shell for a lot more than what I listed. Here is the full list.