[cig-commits] r20646 - in cs/batlab: . trunk/citcom/scripts trunk/citcom/scripts/svn trunk/specfem/scripts trunk/specfem/scripts/svn

[alex at geodynamics.org]

Author: alex
Date: 2012-08-29 19:44:18 -0700 (Wed, 29 Aug 2012)
New Revision: 20646

Modified:
   cs/batlab/README.txt
   cs/batlab/trunk/citcom/scripts/README.txt
   cs/batlab/trunk/citcom/scripts/svn/build.sh
   cs/batlab/trunk/citcom/scripts/svn/simple-make.run-spec
   cs/batlab/trunk/specfem/scripts/README.txt
   cs/batlab/trunk/specfem/scripts/svn/build.sh
Log:
This is the final revisions by Alex Takakuwa.
I have added some mpi support for specfem/citcom, I don't believe relax needs it.
There may be problems, the README files in each scripts folder, as well as the README file at the beginning should give you some information as to where the problems are and how to continue to develop the scripts.

PEACE


Modified: cs/batlab/README.txt
===================================================================
--- cs/batlab/README.txt	2012-08-29 16:39:42 UTC (rev 20645)
+++ cs/batlab/README.txt	2012-08-30 02:44:18 UTC (rev 20646)
@@ -14,4 +14,7 @@
 each scripts directory should have it's own README to describe the info/structure in the scripts.
 /cig/cs/batlab/trunk/citcom/scripts/wgetInstall script was used for local testing.  It is written in bash and is not necessarily compatible with the batlab structure.  However, much of the code was copied into build.sh to build batlab scripts and for that reason it remains, in case more code needs to be copied or restored.
 
+Currently Work:
+The batlab has added mpi to the nodes, however, it is not in the default run path.  Work has to be done on all scripts: citcom, relax, and specfem, to add the path so that the test can find the executable.  So far, this has been started in specfem, but the tests are not working yet.
+
 Gale is no longer needed for testing, as there isn't much dev work going on for the program.

Modified: cs/batlab/trunk/citcom/scripts/README.txt
===================================================================
--- cs/batlab/trunk/citcom/scripts/README.txt	2012-08-29 16:39:42 UTC (rev 20645)
+++ cs/batlab/trunk/citcom/scripts/README.txt	2012-08-30 02:44:18 UTC (rev 20646)
@@ -9,7 +9,15 @@
 
 NOTE: citcom requires MPI which is not on the batlab as of 6/8/2012.  As of now we are simply building a common script, but expecting only to test on ubuntu 10.04.  We are beginning to build our own set of virtual machines on which to test, so that we can install things like MPI as needed.
 
-Currently, the scripts run once a day at midnight.  
+Currently, the scripts are being debugged, and so are not running as cron-jobs.  After they are working correctly, they should be run daily.
 
-We've dropped the following platforms because they do not have MPI:
-x86_64_sol_5.11, x86_64_rhap_6.2, x86_64_sl_6.2, x86_64_deb_6.0, x86_64_macos_10.7, x86_freebsd_7.4, x86_64_fedora_16, x86_64_fedora_15, x86_64_deb_5.0, x86_64_macos_10.7, x86_64_opensuse_11.4, x86_64_rhap_5.7, x86_sl_5.8
+NOTE: 
+debian 5 has an old version of svn, it cannot copy the code from cig.
+
+CURRENT WORK:
+(from specfem)
+All platforms have been given openmpi, which is installed in /usr/lib65/openmpi.  Ubuntu10.10_64 is the exception as that was installed seperately in the default path.  The runs are succeeding for the most part, however, the outcome of each run needs to be checked against a reference file to ensure accuracy.
+However, there are problems:
+freebsd has a bad interpreter for /bin/bash, it seems we may need to use sh (not done yet)
+opensol5.11 still isn't working with mpif90, may need to echo out a `locate mpif90` on that machine and add the path there
+Citcom hasn't been tested, and needs to be with the new scripts (after mpif90 and openmpi) were added to the nodes.  There is no guarantee that it will run on any of the other platforms, or that it has run on those nodes at any point.

Modified: cs/batlab/trunk/citcom/scripts/svn/build.sh
===================================================================
--- cs/batlab/trunk/citcom/scripts/svn/build.sh	2012-08-29 16:39:42 UTC (rev 20645)
+++ cs/batlab/trunk/citcom/scripts/svn/build.sh	2012-08-30 02:44:18 UTC (rev 20646)
@@ -5,6 +5,10 @@
 #cd CitcomS-*  ## this is for wget,
 # cd CitcomS and autoreconf lines are for svn only
 
+# set up mpi
+export PATH=$PATH:/usr/lib64/openmpi # for mpi, which is not installed in the system path
+export PATH=$PATH:/usr/lib64/openmpi/bin/ # for mpif90
+
 # installs and runs citcom, stores results of flux in flux.txt
 cd CitcomS			
 autoreconf -i \

Modified: cs/batlab/trunk/citcom/scripts/svn/simple-make.run-spec
===================================================================
--- cs/batlab/trunk/citcom/scripts/svn/simple-make.run-spec	2012-08-29 16:39:42 UTC (rev 20645)
+++ cs/batlab/trunk/citcom/scripts/svn/simple-make.run-spec	2012-08-30 02:44:18 UTC (rev 20646)
@@ -2,7 +2,7 @@
 run_type = build
 inputs = simple-make.scp, svn-make.svn
 remote_task = build.sh
-platforms = x86_64_ubuntu_10.04.4
+platforms = x86_64_ubuntu_10.04.4, x86_64_sol_5.11, x86_64_rhap_6.2, x86_64_sl_6.2, x86_64_deb_6.0, x86_64_macos_10.7, x86_freebsd_7.4, x86_64_fedora_16, x86_64_fedora_15, x86_64_deb_5.0, x86_64_macos_10.7, x86_64_opensuse_11.4, x86_64_rhap_5.7, x86_sl_5.8
 
 cron_hour = 0
 cron_minute = 0

Modified: cs/batlab/trunk/specfem/scripts/README.txt
===================================================================
--- cs/batlab/trunk/specfem/scripts/README.txt	2012-08-29 16:39:42 UTC (rev 20645)
+++ cs/batlab/trunk/specfem/scripts/README.txt	2012-08-30 02:44:18 UTC (rev 20646)
@@ -6,12 +6,14 @@
 svn script build.sh contains not only the instructions for installation and compilation, but tests with debugging markers, which show up in the batlab error messages.  If there is a problem, notification emails are sent out to emails listed in svn/simple-make.run-spec
 
 
-Currently, the scripts run once a day at midnight.  
+Currently, the scripts are not scheduled tasks as there is debugging to do.  Running them as tasks isn't important until they are running successfully.  After that, they should be run once a day.
 
 
-NOTE: specfem_Globe3D requires MPI which is not on the batlab as of 6/8/2012.  As of now we are simply building a common script, but expecting only to test on ubuntu 10.04.  We are beginning to build our own set of virtual machines on which to test, so that we can install things like MPI as needed.
+NOTE: 
+debian 5 has an old version of svn, it cannot copy the code from cig.
 
-Also, debian 5 seems to be running a version of svn before 1.6, and as such cannot download the necessary files from cig
-
-We've temporarily dropped the following platforms because they do not have MPI:
-x86_64_sol_5.11, x86_64_rhap_6.2, x86_64_sl_6.2, x86_64_deb_6.0, x86_64_macos_10.7, x86_freebsd_7.4, x86_64_fedora_16, x86_64_fedora_15, x86_64_deb_5.0, x86_64_macos_10.7, x86_64_opensuse_11.4, x86_64_rhap_5.7, x86_sl_5.8
+CURRENT WORK:
+All platforms have been given openmpi, which is installed in /usr/lib65/openmpi.  Ubuntu10.10_64 is the exception as that was installed seperately in the default path.  The runs are succeeding for the most part, however, the outcome of each run needs to be checked against a reference file to ensure accuracy.
+However, there are problems:
+freebsd has a bad interpreter for /bin/bash, it seems we may need to use sh (not done yet)
+opensol5.11 still isn't working with mpif90, may need to echo out a `locate mpif90` on that machine and add the path there

Modified: cs/batlab/trunk/specfem/scripts/svn/build.sh
===================================================================
--- cs/batlab/trunk/specfem/scripts/svn/build.sh	2012-08-29 16:39:42 UTC (rev 20645)
+++ cs/batlab/trunk/specfem/scripts/svn/build.sh	2012-08-30 02:44:18 UTC (rev 20646)
@@ -5,6 +5,7 @@
 
 # installs and runs citcom, stores results of flux in flux.txt
 # download the source of only the necessary folders
+OUTPUT=`pwd`
 cd specfem
 svn upgrade			# for opensol5.11, which uses svn 1.7 (the repository is svn 1.6, and it causes some problems)
 svn update --set-depth infinity setup src DATA
@@ -14,6 +15,8 @@
 svn update --set-depth infinity regional_Greece*
 cd ..
 # configure, make and test
+export PATH=$PATH:/usr/lib64/openmpi # for mpi, which is not installed in the system path
+export PATH=$PATH:/usr/lib64/openmpi/bin/ # for mpif90
 ./configure \
     && make all \
     && cd EXAMPLES/regional_Greece_small/ \
@@ -21,6 +24,7 @@
 
 if [ $? != 0 ]			
 then
+    mv config.log $OUTPUT/results.tar.gz
     echo "problem building and running"
     exit 1
 fi