Wednesday, July 9, 2014

Using Check_Openmanage with Check_MK via WATO

In an older post I described the steps to integrate check_openmanage Nagios plugin with check_mk. This approach required manually editing the etc/check_mk/main.mk file to configure the extra_nagios_conf and legacy_checks.

This updated guide uses the check_mk WATO (Web Administration Tool) to integrate the check_openmanage check using a feature called "Active Checks".

Here's the guide, hope it helps:

Environment:

Install Check_openmanage

Unless otherwise specified all paths are relative to the site owners home (ex: /opt/omd/sites/mysite)
  1. Make sure your dell servers had the following SNMP packages installed prior to installing OMSA (if not, it's easy to 'yum remove srvadmin-\*' 'yum install srvadmin-all': net-snmp, net-snmp-libs, net-snmp-utils
    • Start the OMSA services 'srvadmin-services.sh start' and then check 'srvadmin-services.sh status' to verify that the snmpd component is running
    • Ensure that snmpd is running and configured
    • Configure the firewall to allow access from your OMD server to udp port 161
  2. change users on your OMD server to the site user: $ su - mysite
  3. Download the latest check_openmanage from http://folk.uio.no/trondham/software/check_openmanage.html to ~/tmp and extract
  4. copy the check_openmanage script to local/lib/nagios/plugins (this defaults to $USER2$ in your commands)
    
    $ cp tmp/check_openmanage-3.7.11/check_openmanage local/lib/nagios/plugins/
    $ chmod +x local/lib/nagios/plugins/check_openmanage
    
  5. copy the PNP4Nagios template
    
    $ cp tmp/check_openmanage-3.7.11/check_openmanage.php etc/pnp4nagios/templates/
    
  6. Test check_openmanage to see that it can successfully query a node
    
    local/lib/nagios/plugins/check_openmanage -H dell-r720xd-01 -p -C MySecretCommunity
    
    OK - System: 'PowerEdge R720xd', SN: 'XXXXXX1', 24 GB ram (6 dimms), 2 logical drives, 14 physical drives|T0_System_Board_Inlet=21C;42;47 T1_System_Board_Exhaust=30C;70;75 T2_CPU1=48C;86;91 T3_CPU2=39C;86;91 W2_System_Board_Pwr_Consumption=126W;0;0 A0_PS1_Current_1=0.6A;0;0 A1_PS2_Current_2=0.2A;0;0 V25_PS1_Voltage_1=240V;0;0 V26_PS2_Voltage_2=240V;0;0 F0_System_Board_Fan1=2280rpm;0;0 F1_System_Board_Fan2=2280rpm;0;0 F2_System_Board_Fan3=2280rpm;0;0 F3_System_Board_Fan4=3000rpm;0;0 F4_System_Board_Fan5=3600rpm;0;0 F5_System_Board_Fan6=3480rpm;0;0
    
    

WATO Configuration

  1. Create a Host Group by clicking Host Groups under WATO - Configuration, click New Group (click save when done):
    • Name: omsa
    • Alias: Dell OpenManage
  2. Create a Host Tag by clicking Host Tags under WATO - Configuration, click New Tag Group (click save when done):
    • Internal ID: dellomsa
    • Topic: (leave empty)
    • Choices:
      • Tag ID: omsa
      • Description: Dell OpenManage
  3. Create a Active Check by clicking Host & Service Parameter under WATO - Configuration, click Active Checks, click Classical active and passive Nagios checks (create a new one, click save when done):
    • Folder: Main Directory
    • Host Tags: Select Dell OpenManage is set
    • Service Description: check_openmanage
    • Commmand Line: $USER2$/check_openmanage -H $HOSTADDRESS$ -p -C MySecretCommunity
    • Service Description: check_openmanage
    • Check Perfomance Data
  4. Add the omsa Host Tag to a host running OpenManage with SNMP configured by clicking Hosts under WATO - Configuration, and click the properties editor (pencil icon) for the host (click Save & go to Services when done):
    • Host tags: Dell OpenManage: check Dell OpenManage twice

On the Host services page you should see the new service at the bottom, example:
Custom checks (defined via rule)
Status  Checkplugin   Item              Service Description  Plugin output    
OK      custom        check_openmanage  check_openmanage     OK - System: 'PowerEdge R710', SN: 'XXXXXX1', 24 GB ram (6 dimms), 2 logical drives, 14 physical drives
Click Activate Missing services or Save manual check configuration. Activate the changes and you should start seeing the check within a few minutes and graphs after 10 minutes or so. Hope this helps, and comments are welcome.

Tuesday, June 24, 2014

Replace The Foreman Self Signed Certificate with a Trusted Certificate

I've installed a few Foreman servers to provide provisioning and configuration management (via Puppet). This document will cover the steps to replace the self signed certificate used for the web interface with a trusted certificate.

For those unfamiliar with Foreman and Puppet, here are snippet from both project pages (http://theforeman.org/learn_more.html and http://puppetlabs.com/puppet/what-is-puppet:

Foreman is an open source project that helps system administrators manage servers throughout their lifecycle, from provisioning and configuration to orchestration and monitoring. Using Puppet or Chef and Foreman's smart proxy architecture, you can easily automate repetitive tasks, quickly deploy applications, and proactively manage change, both on-premise with VMs and bare-metal or in the cloud.

Foreman provides comprehensive, interaction facilities including a web frontend, CLI and RESTful API which enables you to build higher level business logic on top of a solid foundation.
Puppet is IT automation software that defines and enforces the state of your infrastructure throughout your software development cycle. From provisioning and configuration to orchestration and reporting, from initial code development through production release and updates, Puppet frees sysadmins from writing one-off, fragile scripts and other manual tasks. At the same time, Puppet ensures consistency and dependability across your infrastructure.

With Puppet, repetitive tasks are automated away, so sysadmins can quickly deploy business applications, scaling easily from tens of servers to thousands, both on-premise and in the cloud.

By default, the Puppet / Foreman server install uses Puppet's own internal CA for issuing SSL certificates. The Foreman install defaults to using the Puppet CA self signed cert for the web interface. The following steps will replace The Foreman's SSL certificate for the user web interface, but will leave the Puppet CA and SSL certs in place for Puppet related work.

I spent a bit of time trying to get this working, but each attempt resulted in a working web interface and broken Puppet master to client communications and Foreman proxy. Essentially, I was changing the SSL certificate entries in too many locations. Dominic on the #theforeman channel on FreeNode IRC directed me to this Google Groups thread that listed the short list of places to make the change. The following steps are based on that post.

  1. Create the SSL key and csr
    sudo su - 
    mkdir /root/Incommon-cert
    cd /root/Incommon-cert
    
    openssl req -out $(hostname)-2048.csr -new -newkey rsa:2048 -nodes -keyout $(hostname -f)-2048.key
  2. Copy the contents of the csr to the clipboard and use it to request an InCommon SSL certificate
  3. Once the cert is approved, download the following files to /root/Incommon-cert on the Puppet / Foreman server:
    • as X509 Certificate only, Base64 encoded
    • as X509 Intermediates/root only, Base64 encoded
  4. Rename the files so that we know these are InCommon files
    mv puppet.tld.blah.crt puppet.tld.blah-2048-incommon-cert.crt
    mv puppet.tld.blah_interm.crt puppet.tld.blah-2048-incommon-interm.crt
    chown root:root *.crt
  5. Copy the files to the appropriate directories
    cp puppet.tld.blah-2048.key /var/lib/puppet/ssl/private_keys/
    cp puppet.tld.blah-2048-incommon-cert.crt /var/lib/puppet/ssl/certs/
    cp puppet.tld.blah-2048-incommon-interm.crt /var/lib/puppet/ssl/certs/
  6. Set the appropriate permissions and SELinux configs for the key
    cd /var/lib/puppet/ssl/private_keys/
    chown puppet:puppet *.key
    chmod 640 *.key
    chcon -u system_u -r object_r -t puppet_var_lib_t *.key
    
    ls -lZ
    -rw-r-----. puppet puppet system_u:object_r:puppet_var_lib_t:s0 puppet.tld.blah-2048.key
    -rw-r-----. puppet puppet system_u:object_r:puppet_var_lib_t:s0 puppet.tld.blah.pem
  7. Set perms and SELinux for the certs
    cd /var/lib/puppet/ssl/certs/
    chown puppet:puppet *
    chcon -u system_u -r object_r -t puppet_var_lib_t *.crt
    
    ls -lZ
    -rw-r--r--. puppet puppet system_u:object_r:puppet_var_lib_t:s0 ca.pem
    -rw-r--r--. puppet puppet system_u:object_r:puppet_var_lib_t:s0 incommon-ssl.ca-bundle
    -rw-r--r--. puppet puppet system_u:object_r:puppet_var_lib_t:s0 puppet.tld.blah-2048-incommon-cert.crt
    -rw-r--r--. puppet puppet system_u:object_r:puppet_var_lib_t:s0 puppet.tld.blah-2048-incommon-interm.crt
    -rw-r--r--. puppet puppet system_u:object_r:puppet_var_lib_t:s0 puppet.tld.blah.pem
  8. Next edit the various config files
    • /etc/puppet/node.rb
      --- /etc/puppet/node.rb.orig 2014-03-24 17:48:09.215000045 -0500
      +++ /etc/puppet/node.rb 2014-06-24 10:24:51.049282905 -0500
      @@ -8,7 +8,8 @@
         :facts        => true,          # true/false to upload facts
         :timeout      => 10,
         # if CA is specified, remote Foreman host will be verified
      -  :ssl_ca       => "/var/lib/puppet/ssl/certs/ca.pem",      # e.g. /var/lib/puppet/ssl/certs/ca.pem
      +  #:ssl_ca       => "/var/lib/puppet/ssl/certs/ca.pem",      # e.g. /var/lib/puppet/ssl/certs/ca.pem
      +  :ssl_ca       => "/var/lib/puppet/ssl/certs/puppet.tld.blah-2048-incommon-interm.crt",      # e.g. /var/lib/puppet/ssl/certs/ca.pem
         # ssl_cert and key are required if require_ssl_puppetmasters is enabled in Foreman
         :ssl_cert     => "/var/lib/puppet/ssl/certs/puppet.tld.blah.pem",    # e.g. /var/lib/puppet/ssl/certs/FQDN.pem
         :ssl_key      => "/var/lib/puppet/ssl/private_keys/puppet.tld.blah.pem"      # e.g. /var/lib/puppet/ssl/private_keys/FQDN.pem
    • /usr/lib/ruby/site_ruby/1.8/puppet/reports/foreman.rb
      --- /usr/lib/ruby/site_ruby/1.8/puppet/reports/foreman.rb.orig 2014-03-24 17:44:37.494000046 -0500
      +++ /usr/lib/ruby/site_ruby/1.8/puppet/reports/foreman.rb 2014-06-24 10:28:54.497406986 -0500
      @@ -5,7 +5,8 @@
       # URL of your Foreman installation
       $foreman_url='https://puppet.tld.blah'
       # if CA is specified, remote Foreman host will be verified
      -$foreman_ssl_ca = "/var/lib/puppet/ssl/certs/ca.pem"
      +#$foreman_ssl_ca = "/var/lib/puppet/ssl/certs/ca.pem"
      +$foreman_ssl_ca = "/var/lib/puppet/ssl/certs/puppet.tld.blah-2048-incommon-interm.crt"
       # ssl_cert and key are required if require_ssl_puppetmasters is enabled in Foreman
       $foreman_ssl_cert = "/var/lib/puppet/ssl/certs/puppet.tld.blah.pem"
       $foreman_ssl_key = "/var/lib/puppet/ssl/private_keys/puppet.tld.blah.pem"
    • /etc/httpd/conf.d/05-foreman-ssl.conf
      --- /etc/httpd/conf.d/05-foreman-ssl.conf.orig 2014-06-24 10:30:59.917531640 -0500
      +++ /etc/httpd/conf.d/05-foreman-ssl.conf 2014-06-24 10:32:36.318164714 -0500
      @@ -35,11 +35,18 @@
       
         ## SSL directives
         SSLEngine on
      -  SSLCertificateFile      /var/lib/puppet/ssl/certs/puppet.tld.blah.pem
      -  SSLCertificateKeyFile   /var/lib/puppet/ssl/private_keys/puppet.tld.blah.pem
      -  SSLCertificateChainFile /var/lib/puppet/ssl/certs/ca.pem
      +  SSLCertificateFile      "/var/lib/puppet/ssl/certs/puppet.tld.blah-2048-incommon-cert.crt"
      +  SSLCertificateKeyFile   "/var/lib/puppet/ssl/private_keys/puppet.tld.blah-2048.key"
      +  SSLCertificateChainFile "/var/lib/puppet/ssl/certs/incommon-ssl.ca-bundle"
         SSLCACertificatePath    /etc/pki/tls/certs
         SSLCACertificateFile    /var/lib/puppet/ssl/certs/ca.pem
      +
      +#  SSLCertificateFile      /var/lib/puppet/ssl/certs/puppet.tld.blah.pem
      +#  SSLCertificateKeyFile   /var/lib/puppet/ssl/private_keys/puppet.tld.blah.pem
      +#  SSLCertificateChainFile /var/lib/puppet/ssl/certs/ca.pem
      +#  SSLCACertificatePath    /etc/pki/tls/certs
      +#  SSLCACertificateFile    /var/lib/puppet/ssl/certs/ca.pem
      +
         SSLVerifyClient         optional
         SSLVerifyDepth          3
         SSLOptions +StdEnvVars
  9. Restart the services (foreman-proxy restart probably isn't necessary but may as well)
    service httpd restart
    service foreman-proxy restart

Wednesday, August 28, 2013

Fun with Bash :: Sums

I frequently find the need to sum up long lists of numbers from the Bash command shell. The following is a nice bit of code that sums up the bytes contained in a series of files and prints out the each sum in GB.

The current directory has files *-bytes.log that each contain a single column with a number of bytes on each row, example:

53824
247104
61776
53824
53824
53824
247104
53824
247104
542

The code contains an outer loop to iterate the files and an inner loop to process the contents of the files
for file in $(ls *-bytes.log); do
  sum=0;
  for num in $(cat $file); do
    let sum=$sum+$num;
  done
  echo "$sum/1024/1024/1024" | bc -l | xargs printf "$file %1.2f GB\n";
done

This is an alternative approach using an inner while loop to read the sums rather than cat'ing the file
for file in $(ls *-bytes.log); do
  sum=0;
  while read num; do
    let sum=$sum+$num;
  done < $file
  echo "$sum/1024/1024/1024" | bc -l | xargs printf "$file %1.2f GB\n";
done

Sample results
user1-bytes.log 3.81 GB
user2-bytes.log 4.75 GB
user3-bytes.log 1.40 GB
user4-bytes.log 2.03 GB
user5-bytes.log 5.01 GB
...

I've also found the following bit of code helpful in my $HOME/.bashrc to make quick calculations easy (this comes from a nixCraft Facebook post:

# nixCraft (on Facebook) calc recipe
# Usage: calc "10+2"
#   Pi:  calc "scale=10; 4*a(1)"
# Temperature: calc "30 * 1.8 + 32"
#              calc "(86 - 32)/1.8"
calc() { echo "$*" | bc -l; }

Thursday, June 13, 2013

Building GCC 4.8.1 on CentOS 5.9

References:

Build:

  1. Install packages for dependencies (readline-devel is needed for guile build, dejagnu is needed for gcc make check)
    sudo yum install readline readline-devel guile guile-devel dejagnu expect
    sudo yum -y install readline readline-devel guile guile-devel dejagnu expect
    
  2. Download and untar all the sources
    mkdir -p ~/sources/gcc
    cd ~/sources/gcc
    
    gccver=4.8.1
    gmpver=5.1.2
    mpfrver=3.1.2
    mpcver=1.0.1
    binutilsver=2.23.2
    libtoolver=2.4.2
    libunistringver=0.9.3
    libffiver=3.0.13
    gcver=7.2d
    autogenver=5.17.4
    guilever=2.0.9
    prefixroot=/share/apps/tools
    
    wget http://www.netgull.com/gcc/releases/gcc-4.8.1/gcc-${gccver}.tar.bz2
    wget ftp://ftp.gnu.org/gnu/gmp/gmp-${gmpver}.tar.bz2
    wget http://mpfr.loria.fr/mpfr-current/mpfr-${mpfrver}.tar.bz2
    wget http://www.multiprecision.org/mpc/download/mpc-${mpcver}.tar.gz
    wget http://ftp.gnu.org/gnu/binutils/binutils-${binutilsver}.tar.bz2
    wget http://mirror.sbb.rs/gnu/libtool/libtool-${libtoolver}.tar.gz
    wget http://ftp.gnu.org/gnu/libunistring/libunistring-${libunistringver}.tar.gz
    wget ftp://sourceware.org/pub/libffi/libffi-${libffiver}.tar.gz
    wget http://www.hpl.hp.com/personal/Hans_Boehm/gc/gc_source/gc-${gcver}.tar.gz
    wget http://ftp.gnu.org/gnu/autogen/rel5.17.4/autogen-${autogenver}.tar.gz
    wget ftp://ftp.gnu.org/gnu/guile/guile-${guilever}.tar.gz
    
    for file in *.{gz,bz2}; do echo tar xf $file; done
    
    for dir in `find . -maxdepth 1 -type d | grep -v ^.$ | cut -d \/ -f2` ; do
      app=$(echo $dir | cut -f1 -d-);
      ver=$(echo $dir | cut -f2 -d-);
      mkdir -p ${prefixroot}/${app}/${ver} ;
    done
    
    mv gc-7.2 gc-7.2d
    
  3. Build gmp
    cd gmp-${gmpver}
    mkdir build
    cd build
    .././configure --prefix=${prefixroot}/gmp/${gmpver}
    make
    make check
    make install
    
    EXAMPLE OUTPUT
    ================================================
      Version:           GNU MP 5.1.2
      Host type:         coreisbr-unknown-linux-gnu
      ABI:               64
      Install prefix:    /share/apps/tools/gmp/5.1.2
      Compiler:          gcc -std=gnu99
      Static libraries:  yes
      Shared libraries:  yes
    
    
    Libraries have been installed in:
       /share/apps/gcc/gmp/5.1.2/lib
    
    If you ever happen to want to link against installed libraries
    in a given directory, LIBDIR, you must either use libtool, and
    specify the full pathname of the library, or use the `-LLIBDIR'
    flag during linking and do at least one of the following:
       - add LIBDIR to the `LD_LIBRARY_PATH' environment variable
         during execution
       - add LIBDIR to the `LD_RUN_PATH' environment variable
         during linking
       - use the `-Wl,-rpath -Wl,LIBDIR' linker flag
       - have your system administrator add LIBDIR to `/etc/ld.so.conf'
    
    See any operating system documentation about shared libraries for
    more information, such as the ld(1) and ld.so(8) manual pages.
    
    4. Build mpfr
    cd ../../mpfr-${mpfrver}
    mkdir build
    cd build
    .././configure --prefix=${prefixroot}/mpfr/${mpfrver} \
      --with-gmp=${prefixroot}/gmp/${gmpver}
    make
    make check
    make install
    
    EXAMPLE OUTPUT
    ================================================
    Libraries have been installed in:
       /share/apps/gcc/mpfr/3.1.2/lib
    
    If you ever happen to want to link against installed libraries
    in a given directory, LIBDIR, you must either use libtool, and
    specify the full pathname of the library, or use the `-LLIBDIR'
    flag during linking and do at least one of the following:
       - add LIBDIR to the `LD_LIBRARY_PATH' environment variable
         during execution
       - add LIBDIR to the `LD_RUN_PATH' environment variable
         during linking
       - use the `-Wl,-rpath -Wl,LIBDIR' linker flag
       - have your system administrator add LIBDIR to `/etc/ld.so.conf'
    
    See any operating system documentation about shared libraries for
    more information, such as the ld(1) and ld.so(8) manual pages.
    
  4. Build mpc
    cd ../../mpc-${mpcver}
    mkdir build
    cd build
    .././configure --prefix=${prefixroot}/mpc/${mpcver} \
      --with-gmp=${prefixroot}/gmp/${gmpver} \
      --with-mpfr=${prefixroot}/mpfr/${mpfrver}
    make
    make check
    make install
    
    EXAMPLE OUTPUT
    ================================================
    Libraries have been installed in:
       /share/apps/gcc/mpc/1.0.1/lib
    
    If you ever happen to want to link against installed libraries
    in a given directory, LIBDIR, you must either use libtool, and
    specify the full pathname of the library, or use the `-LLIBDIR'
    flag during linking and do at least one of the following:
       - add LIBDIR to the `LD_LIBRARY_PATH' environment variable
         during execution
       - add LIBDIR to the `LD_RUN_PATH' environment variable
         during linking
       - use the `-Wl,-rpath -Wl,LIBDIR' linker flag
       - have your system administrator add LIBDIR to `/etc/ld.so.conf'
    
    See any operating system documentation about shared libraries for
    more information, such as the ld(1) and ld.so(8) manual pages.
    
  5. Build Binutils
    cd ../../binutils-${binutilsver}
    mkdir build
    cd build
    .././configure --prefix=${prefixroot}/binutils/${binutilsver}
    make
    make check
    make install
    
  6. Build libtool (make check runs for quite a while, upwards of an hour. Runs 126 tests.)
    cd ../../libtool-${libtoolver}
    mkdir build
    cd build
    .././configure --prefix=${prefixroot}/libtool/${libtoolver}
    make
    make check
    make install
    
    EXAMPLE OUTPUT
    ================================================
    ## ------------- ##
    ## Test results. ##
    ## ------------- ##
    
    105 tests behaved as expected.
    21 tests were skipped.
    
  7. Build libunistring
    cd ../../libunistring-${libunistringver}
    mkdir build
    cd build
    .././configure --prefix=${prefixroot}/libunistring/${libunistringver}
    make
    make check
    make install
    
  8. Build libffi
    cd ../../libffi-${libffiver}
    mkdir build
    cd build
    .././configure --prefix=${prefixroot}/libffi/${libffiver}
    make
    make check
    make install
    
    cd ${prefixroot}/libffi/${libffiver}
    ln -s lib/libffi-${libffiver}/include
    cd -
    
    EXAMPLE OUTPUT
    ================================================
    Libraries have been installed in:
       /share/apps/tools/libffi/3.0.13/lib/../lib64
    
    If you ever happen to want to link against installed libraries
    in a given directory, LIBDIR, you must either use libtool, and
    specify the full pathname of the library, or use the `-LLIBDIR'
    flag during linking and do at least one of the following:
       - add LIBDIR to the `LD_LIBRARY_PATH' environment variable
         during execution
       - add LIBDIR to the `LD_RUN_PATH' environment variable
         during linking
       - use the `-Wl,-rpath -Wl,LIBDIR' linker flag
       - have your system administrator add LIBDIR to `/etc/ld.so.conf'
    
    See any operating system documentation about shared libraries for
    more information, such as the ld(1) and ld.so(8) manual pages.
    
  9. Build gc
    cd ../../gc-${gcver}
    mkdir build
    cd build
    .././configure --prefix=${prefixroot}/gc/${gcver}
    make
    make check
    make install
    
    EXAMPLE OUTPUT
    ================================================
    Libraries have been installed in:
       /share/apps/tools/gc/7.2d/lib
    
    If you ever happen to want to link against installed libraries
    in a given directory, LIBDIR, you must either use libtool, and
    specify the full pathname of the library, or use the `-LLIBDIR'
    flag during linking and do at least one of the following:
       - add LIBDIR to the `LD_LIBRARY_PATH' environment variable
         during execution
       - add LIBDIR to the `LD_RUN_PATH' environment variable
         during linking
       - use the `-Wl,-rpath -Wl,LIBDIR' linker flag
       - have your system administrator add LIBDIR to `/etc/ld.so.conf'
    
    See any operating system documentation about shared libraries for
    more information, such as the ld(1) and ld.so(8) manual pages.
    
  10. Build guile. This keeps blowing up with the error following the code. CentOS base repo actually has the guile and guile-devel packages that are new enough to support autogen, so I used the package instead. Leaving this step for future reference.
    cd ../../guile-${guilever}
    mkdir build
    cd build
    .././configure --prefix=${prefixroot}/guile/${guilever} \
       --with-libltdl-prefix=${prefixroot}/libtool/${libtoolver} \
       --with-libgmp-prefix=${prefixroot}/gmp/${gmpver} \
       --with-libunistring-prefix=${prefixroot}/libunistring/${libunistringver} \
       LDFLAGS="-L${prefixroot}/libtool/${libtoolver}/lib -L${prefixroot}/gmp/${gmpver}/lib -L${prefixroot}/libunistring/${libunistringver}/lib -L${prefixroot}/libffi/${libffiver}/lib -L${prefixroot}/gc/${gcver}/lib" \
       CPPFLAGS="-I${prefixroot}/libtool/${libtoolver}/include -I${prefixroot}/libtool/${libtoolver}/include/libltdl -I${prefixroot}/libffi/${libffiver}/include -I${prefixroot}/gc/${gcver}/include -I${prefixroot}/gmp/${gmpver}/include" \
       LIBFFI_CFLAGS=-I${prefixroot}/libffi/${libffiver}/include \
       LIBFFI_LIBS=-L${prefixroot}/libffi/${libffiver}/lib \
       BDW_GC_CFLAGS=-I${prefixroot}/gc/${gcver}/include \
       BDW_GC_LIBS=-L${prefixroot}/gc/${gcver}/lib
    make
    make check
    make install
    
    EXAMPLE OUTPUT
    ================================================
    make[1]: Entering directory `/home/mhanby/sources/gcc/guile-2.0.9/build'
    Making all in lib
    make[2]: Entering directory `/home/mhanby/sources/gcc/guile-2.0.9/build/lib'
    make  all-recursive
    make[3]: Entering directory `/home/mhanby/sources/gcc/guile-2.0.9/build/lib'
    make[4]: Entering directory `/home/mhanby/sources/gcc/guile-2.0.9/build/lib'
    make[4]: Nothing to be done for `all-am'.
    make[4]: Leaving directory `/home/mhanby/sources/gcc/guile-2.0.9/build/lib'
    make[3]: Leaving directory `/home/mhanby/sources/gcc/guile-2.0.9/build/lib'
    make[2]: Leaving directory `/home/mhanby/sources/gcc/guile-2.0.9/build/lib'
    Making all in meta
    make[2]: Entering directory `/home/mhanby/sources/gcc/guile-2.0.9/build/meta'
    make[2]: Nothing to be done for `all'.
    make[2]: Leaving directory `/home/mhanby/sources/gcc/guile-2.0.9/build/meta'
    Making all in libguile
    make[2]: Entering directory `/home/mhanby/sources/gcc/guile-2.0.9/build/libguile'
    make  all-am
    make[3]: Entering directory `/home/mhanby/sources/gcc/guile-2.0.9/build/libguile'
      CC       libguile_2.0_la-finalizers.lo
    ../.././libguile/finalizers.c:167: error: static declaration of 'GC_set_finalizer_notifier' follows non-static declaration
    /share/apps/tools/gc/7.2d/include/gc/gc.h:177: error: previous declaration of 'GC_set_finalizer_notifier' was here
    make[3]: *** [libguile_2.0_la-finalizers.lo] Error 1
    make[3]: Leaving directory `/home/mhanby/sources/gcc/guile-2.0.9/build/libguile'
    make[2]: *** [all] Error 2
    make[2]: Leaving directory `/home/mhanby/sources/gcc/guile-2.0.9/build/libguile'
    make[1]: *** [all-recursive] Error 1
    make[1]: Leaving directory `/home/mhanby/sources/gcc/guile-2.0.9/build'
    make: *** [all] Error 2
    
  11. Build autogen
    cd ../../autogen-${autogenver}
    mkdir build
    cd build
    .././configure --prefix=${prefixroot}/autogen/${autogenver}
    make
    make check
    make install
    
    EXAMPLE OUTPUT
    ================================================
    ------------------------------------------------------------------------
    Configuration:
    
      Source code location:   ../.
      Compiler:               gcc -std=gnu99
      Compiler flags:         -g -O2
      Host System Type:       x86_64-unknown-linux-gnu
      Install path:           /share/apps/tools/autogen/5.17.4
    
      See config.h for further configuration information.
    ------------------------------------------------------------------------
    
    Libraries have been installed in:
       /share/apps/tools/autogen/5.17.4/lib
    
    If you ever happen to want to link against installed libraries
    in a given directory, LIBDIR, you must either use libtool, and
    specify the full pathname of the library, or use the `-LLIBDIR'
    flag during linking and do at least one of the following:
       - add LIBDIR to the `LD_LIBRARY_PATH' environment variable
         during execution
       - add LIBDIR to the `LD_RUN_PATH' environment variable
         during linking
       - use the `-Wl,-rpath -Wl,LIBDIR' linker flag
       - have your system administrator add LIBDIR to `/etc/ld.so.conf'
    
    See any operating system documentation about shared libraries for
    more information, such as the ld(1) and ld.so(8) manual pages.
    
  12. Build gcc (make took approximately 2.5 hours to run on a system with a 2.7GHz Intel Xeon E5-2680, make check took about 3 hours)
    cd ../../gcc-${gccver}
    mkdir build
    cd build
    
    OLD_LD_LIBRARY_PATH=${LD_LIBRARY_PATH}
    export LD_LIBRARY_PATH=${prefixroot}/gmp/${gmpver}/lib:${prefixroot}/mpc/${mpcver}/lib:${prefixroot}/mpfr/${mpfrver}/lib:${LD_LIBRARY_PATH}
    
    .././configure \
      --prefix=${prefixroot}/gcc/${gccver} \
      --with-gmp=${prefixroot}/gmp/${gmpver} \
      --with-mpfr=${prefixroot}/mpfr/${mpfrver} \
      --with-mpc=${prefixroot}/mpc/${mpcver} \
      LD_FOR_TARGET=ld \
      AS_FOR_TARGET=as \
      --with-ld=${prefixroot}/binutils/${binutilsver}/bin/ld \
      --with-as=${prefixroot}/binutils/${binutilsver}/bin/as \
      --with-ar=${prefixroot}/binutils/${binutilsver}/bin/ar \
      AR_FOR_TARGET=ar
    
    time make
    
    #real 150m4.427s
    #user 101m21.408s
    #sys 12m54.047s
    
    OLD_PATH=${PATH}
    export PATH=/share/apps/tools/autogen/5.17.4/bin:${PATH}
    time make -k check
    make install
    
    export PATH=${OLD_PATH}
    export LD_LIBRARY_PATH=${OLD_LD_LIBRARY_PATH}
    
    EXAMPLE OUTPUT
    ================================================
    ----------------------------------------------------------------------
    Libraries have been installed in:
       /share/apps/tools/gcc/4.8.1/lib/../lib
    
    If you ever happen to want to link against installed libraries
    in a given directory, LIBDIR, you must either use libtool, and
    specify the full pathname of the library, or use the `-LLIBDIR'
    flag during linking and do at least one of the following:
       - add LIBDIR to the `LD_LIBRARY_PATH' environment variable
         during execution
       - add LIBDIR to the `LD_RUN_PATH' environment variable
         during linking
       - use the `-Wl,-rpath -Wl,LIBDIR' linker flag
       - have your system administrator add LIBDIR to `/etc/ld.so.conf'
    
    See any operating system documentation about shared libraries for
    more information, such as the ld(1) and ld.so(8) manual pages.
    ----------------------------------------------------------------------
    
    ----------------------------------------------------------------------
    Libraries have been installed in:
       /share/apps/tools/gcc/4.8.1/lib/../lib64
    
    If you ever happen to want to link against installed libraries
    in a given directory, LIBDIR, you must either use libtool, and
    specify the full pathname of the library, or use the `-LLIBDIR'
    flag during linking and do at least one of the following:
       - add LIBDIR to the `LD_LIBRARY_PATH' environment variable
         during execution
       - add LIBDIR to the `LD_RUN_PATH' environment variable
         during linking
       - use the `-Wl,-rpath -Wl,LIBDIR' linker flag
       - have your system administrator add LIBDIR to `/etc/ld.so.conf'
    
    See any operating system documentation about shared libraries for
    more information, such as the ld(1) and ld.so(8) manual pages.
    ----------------------------------------------------------------------
    
  13. Create the module file (for Environment Modules support)
    #%Module1.0####################################################################
    ##
    ## mymodule modulefile
    ##
    ## Sets up the 4.8.1 GCC compilation environment
    ##
    set ver [lrange [split [ module-info name ] / ] 1 1 ]
    set name [lrange [split [ module-info name ] / ] 0 0 ]
    set loading [module-info mode load]
    set subname [lrange [split $name - ] 0 0 ]
    
    proc ModulesHelp { } {
      puts stderr "\tThis module sets the environment for $name v$ver"
    }
    
    module-whatis   "Set environment variables to use $name version $ver"
    
    conflict compiler
    
    set base /share/apps/tools
    set gccdir $base/$subname/$ver
    set binutilsdir $base/binutils/2.23.2
    set gmpdir $base/gmp/5.1.2
    set mpcdir $base/mpc/1.0.1
    set mpfrdir $base/mpfr/3.1.2
    
    ## Add bin directories to the path
    prepend-path PATH $gccdir/bin
    prepend-path PATH $binutilsdir/bin
    
    prepend-path LD_LIBRARY_PATH $mpfrdir/lib
    prepend-path LD_LIBRARY_PATH $mpcdir/lib
    prepend-path LD_LIBRARY_PATH $gmpdir/lib
    prepend-path LD_LIBRARY_PATH $binutilsdir/lib
    prepend-path LD_LIBRARY_PATH $binutilsdir/lib64
    prepend-path LD_LIBRARY_PATH $gccdir/lib
    prepend-path LD_LIBRARY_PATH $gccdir/lib64
    
    prepend-path MANPATH $gccdir/share/man
    prepend-path C_INCLUDE_PATH $gccdir/include
    prepend-path CPLUS_INCLUDE_PATH $gccdir/include
    
    setenv CC $gccdir/bin/gcc
    setenv CXX $gccdir/bin/g++
    setenv FC $gccdir/bin/gfortran
    
    if { [ module-info mode load ] } {
      puts stderr "Note: $name $ver environment loaded."
    }
    

Friday, April 19, 2013

How To Compile Gromacs 4.6.1 with OpenMPI 1.6.4 on CentOS

I took the following notes while installing Gromacs 4.6.1 recently. Hopefully others will find them useful. The software was compiled and installed on a CentOS 5.9 x86_64 containing QDR Infiniband. The system uses SGE (Grid Engine) as it's scheduler. Intel compilers 13.1.1 were used to compile both OpenMPI and Gromacs.

Intel Compilers

I used version 13.1.1 of the Intel compilers. I'm including the module file here for reference
#%Module

set ver 13.1.1
set arch intel64

set root /share/apps/intel/parallel_studio_xe_2013_update3/composer_xe_2013.3.163
set ccroot /opt/intel/Compiler/$ver/$ccver
set fcroot /opt/intel/Compiler/$ver/$fcver
set mklroot $root/mkl

set msg "This module adds Intel compilers v$ver to various paths"

proc ModulesHelp { } {
   puts stderr $msg
}

module-whatis   $msg

setenv MKLROOT $mklroot
prepend-path MANPATH $root/man/en_US
prepend-path INTEL_LICENSE_FILE $root/licenses

prepend-path NLSPATH $root/compiler/lib/$arch/locale/en_US:$root/ipp/lib/$arch/locale/en_US:$root/mkl/lib/$arch/locale/en_US:$root/debugger/lib/$arch/locale/en_US

prepend-path LIBRARY_PATH $root/compiler/lib/$arch:$root/ipp/lib/$arch:$root/mkl/lib/$arch:$root/tbb/lib/$arch/gcc4.1
prepend-path MIC_LD_LIBRARY_PATH $root/compiler/lib/mic:$root/mkl/lib/mic:$root/tbb/lib/mic
prepend-path LD_LIBRARY_PATH $root/compiler/lib/$arch:$root/mpirt/lib/$arch:$root/ipp/lib/$arch:$root/mkl/lib/$arch:$root/tbb/lib/$arch/gcc4.1
prepend-path PATH $root/bin/$arch:$root/mpirt/bin/$arch:$root/bin/${arch}_mic:$root/debugger/gui/$arch

prepend-path CPATH $root/mkl/include:$root/tbb/include
prepend-path INCLUDE $root/mkl/include

prepend-path IPPROOT $root/ipp
prepend-path TBBROOT $root/tbb
prepend-path IDB_HOME $root/bin/$arch

Build OpenMPI 1.6.4

First, build the latest OpenMPI with the Intel compilers. This version of OpenMPI will reside in the Gromacs 4.6.1 install path.
  1. Create the install base directory
    cd /share/apps/gromacs/4.6.1/build
    wget http://www.open-mpi.org/software/ompi/v1.6/downloads/openmpi-1.6.4.tar.bz2
    
  2. Create the build script for Intel compilers: /share/apps/gromacs/4.6.1/build/build-openmpi-intel.sh
    #!/bin/sh
    . /etc/profile.d/modules.sh
    ver=1.6
    rel=1.6.4
    grover=4.6.1
    src="openmpi-${rel}.tar.bz2"
    url="http://www.open-mpi.org/software/ompi/v${ver}/downloads/${src}"
    compiler="intel"
    basedir="/share/apps/gromacs/${grover}/openmpi"
    prefix="${basedir}/${rel}-${compiler}"
    
    if [ -d $prefix ]; then
      echo "Installation directory already exists, exiting to prevent overwrite: $prefix";
      exit 1
    else
      echo "Verified installation directory does not exist: $prefix"
    fi
    
    if [ ! -f $src ]; then
      echo "Downloading source code from: $url";
      wget $url;
    else
      echo "Using existing source code: $src";
    fi
    
    if [ -d "openmpi-${rel}" ]; then
      echo "Removing existing build directory ./openmpi-${rel}"
      rm -rf openmpi-${rel};
    fi
    
    echo "Extracting $src"
    tar -jxf $src
    cd openmpi-${rel}
    
    echo "Building OpenMPI $rel for Intel compilers"
    echo "Running configure"
    module purge
    module load intel/intel-compilers-13.1.1
    CC=icc CXX=icpc F77=ifort FC=ifort ./configure --with-sge --with-openib --prefix=$prefix --enable-static --enable-shared
    
    make all install
    module purge
    
    cd ..
    
  3. Run the compile and install
    ./build-openmpi-intel.sh | tee openmpi-1.6.4-intel.log
    
  4. Create the module file (based off of [http://www.levlafayette.com/node/145 this example]) in the Gromacs base directory
    mkdir -p /share/apps/gromacs/4.6.1/modulefiles/gromacs-openmpi-intel
    vim /share/apps/gromacs/4.6.1/modulefiles/gromacs-openmpi-intel/1.6.4
    
    #%Module1.0#####################################################################
    ##
    ## $name modulefile
    ##
    # /share/apps/gromacs/4.6.1/openmpi/1.6.4-intel/bin
    # /share/apps/gromacs/4.6.1/openmpi/gromacs-openmpi-intel/1.6.4-intel/bin
    set ver [lrange [split [ module-info name ] / ] 1 1 ]
    set name [lrange [split [ module-info name ] / ] 0 0 ]
    set loading [module-info mode load]
    set subname [lrange [split $name - ] 0 0 ]
    #set compiler [lrange [split $name - ] 1 1 ]
    set compiler "intel"
    set compilerver "13.1.1"
    
    proc ModulesHelp { } {
      puts stderr "\tThis module sets the envinronment for $name v$ver compiled\n\twith Intel v13.1.1 compilers"
    }
    
    module-whatis   "Set environment variables to use $name version $ver"
    
    if { $loading && ![ is-loaded $compiler/$compilerver ] } {
      module load $compiler/$compilerver
    }
    
    set basedir /share/apps/gromacs/4.6.1/openmpi/${ver}-$compiler
    
    prepend-path --delim " " CPPFLAGS -I$basedir/include
    prepend-path --delim " " LDFLAGS -L$basedir/lib
    
    prepend-path LD_LIBRARY_PATH $basedir/lib
    prepend-path MANPATH $basedir/share/man
    prepend-path PATH $basedir/bin
    
    setenv  MPI_DIR         $basedir/
    setenv  MPI_HOME        $basedir/
    setenv  OPENMPI_ROOT    $basedir/
    
  5. Run a test
    • Create the input C file /share/apps/openmpi/build/mpi-helloworld.c
      #include <stdio>
      #include <string>
      #include <stddef>
      #include <stdlib>
      #include "mpi.h"
      
      main(int argc, char **argv ) {
          int rank, size;
          int buflen = 512;
          char name[buflen];
          
          MPI_Init(&argc, &argv);
          MPI_Comm_size(MPI_COMM_WORLD,&size);
          MPI_Comm_rank(MPI_COMM_WORLD, &rank);
      
          gethostname(name, buflen);
          
          printf( "P rank %d of %d, host %s\n", rank, size, name);
      
          MPI_Finalize();
      }
      
    • Compile mpi-helloworld.c
      module load /share/apps/gromacs/4.6.1/modulefiles/gromacs-openmpi-intel/1.6.4
      mpicc -o mpi-helloworld-intel mpi-helloworld.c
      
    • run it as a job
      module purge
      module load /share/apps/gromacs/4.6.1/modulefiles/gromacs-openmpi-intel/1.6.4
      qsub -V -b y \
         -l h_rt=00:15:00 \
         -l vf=256M \
         -j y \
         -pe openmpi\* 8 \
         mpirun -n 8 /share/apps/openmpi/build/mpi-helloworld-intel  
      

Build Gromacs 4.6.1

Official Gromacs 4.6 build instructions They have changed dramatically from versions 4.5 and prior. One requirement listed is that we need CMake version 2.8 or later. EPEL provides CMake 2.6.4, so we'll need to build CMake from scratch.
  1. Download the latest CMake from here: http://www.cmake.org/cmake/resources/software.html
    sudo mkdir /share/apps/cmake
    sudo chown mhanby:atlab /share/apps/cmake
    cd /share/apps/cmake
    wget http://www.cmake.org/files/v2.8/cmake-2.8.10.2-Linux-i386.tar.gz
    tar -zxf cmake-2.8.10.2-Linux-i386.tar.gz 
    
  2. Create the build directory and download the source
    mkdir -p /share/apps/gromacs/4.6.1/build
    cd /share/apps/gromacs/4.6.1/build
    wget ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.1.tar.gz
    tar -zxf gromacs-4.6.1.tar.gz 
    mkdir gromacs-4.6.1/build
    cd gromacs-4.6.1/build
    
  3. Create the module files
    mkdir /share/apps/modulefiles/gromacs-intel
    vim /share/apps/modulefiles/gromacs-intel/4.6.1
    
    #%Module
    
    set ver 4.6.1
    set app "Gromacs"
    set url "http://gromacs.org/"
    set approot /share/apps/gromacs/$ver
    set msg "This module adds $app v$ver to various paths\nWebsite: $url\n\n"
    
    proc ModulesHelp { } {
       puts stderr $msg
    }
    
    module-whatis  $msg
    
    module use --append $approot/modulefiles
    module load intel/13.1.1
    #module load $approot/modulefiles/gromacs-openmpi-intel/1.6.4
    module load gromacs-openmpi-intel/1.6.4
    
    setenv GROMACSHOME $approot
    #setenv MKL_HOME $::env(MKLROOT)
    prepend-path PATH $approot/bin
    prepend-path LD_LIBRARY_PATH $approot/lib
    prepend-path MANPATH $approot/man
    prepend-path MODULEPATH $approot/modulefiles
    prepend-path PKG_CONFIG_PATH $approot/lib/pkgconfig
    
  4. The next steps will build single and double precision in serial and parallel
    • Serial single precision
      1. Run cmake to configure the build
        module purge
        module load gromacs-intel/4.6.1
        export PATH=/share/apps/cmake/cmake-2.8.10.2-Linux-i386/bin:$PATH
        
        cd /share/apps/gromacs/4.6.1/build/gromacs-4.6.1/build
        rm -rf *
        
        cmake .. \
           -DCMAKE_C_COMPILER=icc \
           -DCMAKE_CXX_COMPILER=icpc \
           -DGMX_BUILD_OWN_FFTW=ON \
           -DCMAKE_INSTALL_PREFIX=/share/apps/gromacs/4.6.1 \
           -DREGRESSIONTEST_DOWNLOAD=ON
        
      2. View the configuration
        ccmake ..
        
         BUILD_SHARED_LIBS                ON
         CMAKE_BUILD_TYPE                 Release
         CMAKE_INSTALL_PREFIX             /share/apps/gromacs/4.6.1
         CMAKE_PREFIX_PATH
         CUDA_HOST_COMPILER               /share/apps/intel/parallel_studio_xe_2013_update3/composer_xe_2013.3.163/bin/intel64/icc
         GMX_CPU_ACCELERATION             SSE4.1
         GMX_DEFAULT_SUFFIX               ON
         GMX_DOUBLE                       OFF
         GMX_FFT_LIBRARY                  fftw3
         GMX_GPU                          OFF
         GMX_GSL                          OFF
         GMX_MPI                          OFF
         GMX_OPENMP                       ON
         GMX_QMMM_PROGRAM                 none
         GMX_THREAD_MPI                   ON
         GMX_X11                          OFF
         REGRESSIONTEST_DOWNLOAD          OFF                              
        
      3. make
        make
        
      4. Run the tests
        make check
        [ 70%] Built target gmx
        [ 71%] Built target gmxfftw
        [ 80%] Built target md
        [ 92%] Built target gmxana
        [ 92%] Built target editconf
        [ 96%] Built target gmxpreprocess
        [ 97%] Built target grompp
        [ 97%] Built target pdb2gmx
        [ 97%] Built target gmxcheck
        [100%] Built target mdrun
        [100%] Built target gmxtests
        Test project /share/apps/gromacs/4.6.1/build/gromacs-4.6.1/build
            Start 1: regressiontests/simple
        1/5 Test #1: regressiontests/simple ...........   Passed   72.17 sec
            Start 2: regressiontests/complex
        2/5 Test #2: regressiontests/complex ..........   Passed  868.76 sec
            Start 3: regressiontests/kernel
        3/5 Test #3: regressiontests/kernel ...........   Passed  583.48 sec
            Start 4: regressiontests/freeenergy
        4/5 Test #4: regressiontests/freeenergy .......   Passed  695.84 sec
            Start 5: regressiontests/pdb2gmx
        5/5 Test #5: regressiontests/pdb2gmx ..........   Passed  379.29 sec
        
        100% tests passed, 0 tests failed out of 5
        
        Total Test time (real) = 2599.69 sec
        [100%] Built target check
        
      5. Install
        make install
        
        ...
        -- Installing: /share/apps/gromacs/4.6.1/lib/pkgconfig/libgmxana.pc
        -- Installing: /share/apps/gromacs/4.6.1/bin/GMXRC
        -- Installing: /share/apps/gromacs/4.6.1/bin/GMXRC.bash
        -- Installing: /share/apps/gromacs/4.6.1/bin/GMXRC.zsh
        -- Installing: /share/apps/gromacs/4.6.1/bin/GMXRC.csh
        -- Installing: /share/apps/gromacs/4.6.1/bin/completion.csh
        -- Installing: /share/apps/gromacs/4.6.1/bin/completion.bash
        -- Installing: /share/apps/gromacs/4.6.1/bin/completion.zsh
        -- Installing: /share/apps/gromacs/4.6.1/bin/demux.pl
        -- Installing: /share/apps/gromacs/4.6.1/bin/xplor2gmx.pl
        
    • Serial double precision (will append _d to applicable installed files, example, mdrun_d)
      1. Run cmake to configure the build
        module purge
        module load gromacs-intel/4.6.1
        export PATH=/share/apps/cmake/cmake-2.8.10.2-Linux-i386/bin:$PATH
        
        cd /share/apps/gromacs/4.6.1/build/gromacs-4.6.1/build
        rm -rf *
        
        cmake .. \
           -DCMAKE_C_COMPILER=icc \
           -DCMAKE_CXX_COMPILER=icpc \
           -DGMX_BUILD_OWN_FFTW=ON \
           -DGMX_DOUBLE=ON \
           -DCMAKE_INSTALL_PREFIX=/share/apps/gromacs/4.6.1 \
           -DREGRESSIONTEST_DOWNLOAD=ON
        
      2. View the configuration
        ccmake ..
        
         BUILD_SHARED_LIBS                ON
         CMAKE_BUILD_TYPE                 Release
         CMAKE_INSTALL_PREFIX             /share/apps/gromacs/4.6.1
         CMAKE_PREFIX_PATH
         GMX_CPU_ACCELERATION             SSE4.1
         GMX_DEFAULT_SUFFIX               ON
         GMX_DOUBLE                       ON
         GMX_FFT_LIBRARY                  fftw3
         GMX_GPU                          OFF
         GMX_GSL                          OFF
         GMX_MPI                          OFF
         GMX_OPENMP                       ON
         GMX_QMMM_PROGRAM                 none
         GMX_THREAD_MPI                   ON
         GMX_X11                          OFF
         REGRESSIONTEST_DOWNLOAD          OFF
        
      3. make
        make
        
      4. Run the tests
        make check
        
        Test project /share/apps/gromacs/4.6.1/build/gromacs-4.6.1/build
            Start 1: regressiontests/simple
        1/5 Test #1: regressiontests/simple ...........   Passed    3.33 sec
            Start 2: regressiontests/complex
        2/5 Test #2: regressiontests/complex ..........   Passed    6.80 sec
            Start 3: regressiontests/kernel
        3/5 Test #3: regressiontests/kernel ...........   Passed   52.89 sec
            Start 4: regressiontests/freeenergy
        4/5 Test #4: regressiontests/freeenergy .......   Passed    9.19 sec
            Start 5: regressiontests/pdb2gmx
        5/5 Test #5: regressiontests/pdb2gmx ..........   Passed   22.82 sec
        
        100% tests passed, 0 tests failed out of 5
        
        Total Test time (real) =  95.08 sec
        [100%] Built target check
        
      5. Install
        make install
        
    • Parallel single precision (will append _mpi to applicable installed files, example, mdrun_mpi)
      1. Run cmake to configure the build
        module purge
        module load gromacs-intel/4.6.1
        export PATH=/share/apps/cmake/cmake-2.8.10.2-Linux-i386/bin:$PATH
        
        cd /share/apps/gromacs/4.6.1/build/gromacs-4.6.1/build
        rm -rf *
        
        cmake .. \
           -DCMAKE_C_COMPILER=icc \
           -DCMAKE_CXX_COMPILER=icpc \
           -DGMX_BUILD_OWN_FFTW=ON \
           -DGMX_MPI=ON \
           -DCMAKE_INSTALL_PREFIX=/share/apps/gromacs/4.6.1 \
           -DREGRESSIONTEST_DOWNLOAD=ON
        
      2. View the configuration
        ccmake ..
        
         BUILD_SHARED_LIBS                ON
         CMAKE_BUILD_TYPE                 Release
         CMAKE_INSTALL_PREFIX             /share/apps/gromacs/4.6.1
         CMAKE_PREFIX_PATH
         CUDA_HOST_COMPILER               /share/apps/intel/parallel_studio_xe_2013_update3/composer_xe_2013.3.163/bin/intel64/icc
         GMX_CPU_ACCELERATION             SSE4.1
         GMX_DEFAULT_SUFFIX               ON
         GMX_DOUBLE                       OFF
         GMX_FFT_LIBRARY                  fftw3
         GMX_GPU                          OFF
         GMX_GSL                          OFF
         GMX_MPI                          ON
         GMX_OPENMP                       ON
         GMX_QMMM_PROGRAM                 none
         GMX_THREAD_MPI                   OFF
         GMX_X11                          OFF
         MPI_EXTRA_LIBRARY                /usr/lib64/librdmacm.so;/usr/lib64/libibverbs.so;/usr/lib64/librt.so;/usr/lib64/libnsl.so;/usr/lib64/libutil.so;/usr/lib64/libdl.so;/usr/lib64/libm.so;/usr/lib64/librt.so;
         MPI_LIBRARY                      /share/apps/gromacs/4.6.1/openmpi/1.6.4-intel/lib/libmpi.so
         REGRESSIONTEST_DOWNLOAD          OFF
        
      3. make
        make
        
      4. Run the tests
        make check
        
        Test project /share/apps/gromacs/4.6.1/build/gromacs-4.6.1/build
            Start 1: regressiontests/simple
        1/5 Test #1: regressiontests/simple ...........   Passed   22.68 sec
            Start 2: regressiontests/complex
        2/5 Test #2: regressiontests/complex ..........   Passed   29.49 sec
            Start 3: regressiontests/kernel
        3/5 Test #3: regressiontests/kernel ...........   Passed  222.08 sec
            Start 4: regressiontests/freeenergy
        4/5 Test #4: regressiontests/freeenergy .......   Passed   19.17 sec
            Start 5: regressiontests/pdb2gmx
        5/5 Test #5: regressiontests/pdb2gmx ..........   Passed   75.39 sec
        
        100% tests passed, 0 tests failed out of 5
        
        Total Test time (real) = 368.83 sec
        [100%] Built target check
        
      5. Install
        make install
        
    • Parallel double precision (will append _mpi_d to applicable installed files, example, mdrun_mpi_d)
      1. Run cmake to configure the build
        module purge
        module load gromacs-intel/4.6.1
        export PATH=/share/apps/cmake/cmake-2.8.10.2-Linux-i386/bin:$PATH
        
        cd /share/apps/gromacs/4.6.1/build/gromacs-4.6.1/build
        rm -rf *
        
        cmake .. \
           -DCMAKE_C_COMPILER=icc \
           -DCMAKE_CXX_COMPILER=icpc \
           -DGMX_BUILD_OWN_FFTW=ON \
           -DGMX_MPI=ON \
           -DGMX_DOUBLE=ON \
           -DCMAKE_INSTALL_PREFIX=/share/apps/gromacs/4.6.1 \
           -DREGRESSIONTEST_DOWNLOAD=ON
        
      2. View the configuration
        ccmake ..
        
         BUILD_SHARED_LIBS                ON 
         CMAKE_BUILD_TYPE                 Release
         CMAKE_INSTALL_PREFIX             /share/apps/gromacs/4.6.1
         CMAKE_PREFIX_PATH
         GMX_CPU_ACCELERATION             SSE4.1
         GMX_DEFAULT_SUFFIX               ON
         GMX_DOUBLE                       ON
         GMX_FFT_LIBRARY                  fftw3
         GMX_GPU                          OFF
         GMX_GSL                          OFF
         GMX_MPI                          ON
         GMX_OPENMP                       ON
         GMX_QMMM_PROGRAM                 none
         GMX_THREAD_MPI                   OFF
         GMX_X11                          OFF
         MPI_EXTRA_LIBRARY                /usr/lib64/librdmacm.so;/usr/lib64/libibverbs.so;/usr/lib64/librt.so;/usr/lib64/libnsl.so;/usr/lib64/libutil.so;/usr/lib64/libdl.so;/usr/lib64/libm.so;/usr/lib64/librt.so;/usr/lib64/libnsl.so;/usr/lib64/libutil.so                       
         MPI_LIBRARY                      /share/apps/gromacs/4.6.1/openmpi/1.6.4-intel/lib/libmpi.so
         REGRESSIONTEST_DOWNLOAD          OFF
        
      3. make
        make
        
      4. Run the tests
        make check
        
        Test project /share/apps/gromacs/4.6.1/build/gromacs-4.6.1/build
            Start 1: regressiontests/simple
        1/5 Test #1: regressiontests/simple ...........   Passed   22.65 sec
            Start 2: regressiontests/complex
        2/5 Test #2: regressiontests/complex ..........   Passed   32.25 sec
            Start 3: regressiontests/kernel
        3/5 Test #3: regressiontests/kernel ...........   Passed  232.23 sec
            Start 4: regressiontests/freeenergy
        4/5 Test #4: regressiontests/freeenergy .......   Passed   21.13 sec
            Start 5: regressiontests/pdb2gmx
        5/5 Test #5: regressiontests/pdb2gmx ..........   Passed   82.39 sec
        
        100% tests passed, 0 tests failed out of 5
        
        Total Test time (real) = 390.67 sec
        [100%] Built target check
        
      5. Install
        make install
        

Wednesday, February 27, 2013

Ubuntu 13.04 on Google Nexus 7

Canonical has recently released a developer preview of Ubuntu 13.04 for Google Nexus devices.

I figured, what the heck, may as well try it out on my Google Nexus 7. Following these instructions, the installation went off without a hitch.

I used a laptop running Ubuntu 12.10 to perform the installation.

Following the installation, I ran into the issue during First Boot where the on screen keyboard didn't work. I don't have an OTG adapter cable, but do have a Bluetooth Logitech Android tablet keyboard. As stated in the instructions, the Bluetooth keyboard doesn't work during first boot.

That is, initially :-)

I got around this by clicking the Gear icon in the upper right corner and clicking System Settings -> Bluetooth. I clicked the add button and put the keyboard into connect mode. The keyboard successfully synced with the tablet.

Great, however now I couldn't find a way to close the System Settings window. I could move it around, but couldn't get the focus away and back to the First Boot screen.

No problem, click the Gear icon again and select restart. Upon reboot, the Bluetooth keyboard works fine on the First Boot windows.

Wednesday, January 23, 2013

How To: Recursively Create Numeric Directories

I was asked by a colleague how to do the following:

I have a root folder that I need to create a directory based on job numbers.

From the root folder, I'd like to create the following:

1000
1000\1100
1000\1100\1101
1000\1100\1102

all the way up to 

9000\9900\9999

To explain, I'll use the 5000 folder:

I would need:
5000
5000\5100
5000\5100\5101 through 5000\5100\5199
5000\5200
5000\5200\5201 through 5200\5200\5299
and so on.

What would be the easiest way?

The solution isn't a big deal for anyone familiar with scripting, but I figured I'd share here in case other none coders need help with a similar problem.

I wasn't sure whether they were on a Windows computer (figured most likely based on the slashes) or Linux / Mac, so I provided both a Bash and Windows command shell solutions.

There are any number of ways to approach this, I chose nested for loops.

First the Bash solution:

for x in {1..9}; do
  mkdir ${x}000
  cd ${x}000
  for y in {1..9}; do
    mkdir ${x}${y}00
    cd ${x}${y}00
    for ((z=1; z<=99; z+=1)); do
      mkdir `printf "%s%s%02d" $x $y $z`
    done
    cd ..
  done
  cd ..
done

Now the Windows solution:

setlocal EnableDelayedExpansion
for /l %x in (1, 1, 9) do (
  mkdir %x000
  cd %x000
  for /l %y in (1, 1, 9) do (
    mkdir %x%y00
    cd %x%y00
    for /l %z in (1, 1, 99) do (
      if %z LSS 10 (
        mkdir %x%y0%z
      ) else (
        mkdir %x%y%z
      )
    )
    cd ..
  )
  cd ..  
)