creating grid in Travis

.travis.yml

@@ -1,5 +1,5 @@
 # Check on http://lint.travis-ci.org/ after modifying it!
-sudo: false
+sudo: required
 language: c
 os:
   - linux
@@ -22,6 +22,11 @@ before_install:
   - conda update -q conda
   # Useful for debugging any issues with conda
   - conda info -a
+  # install a grid system in Travis
+  - travis/install_sge.sh
+  - export SGE_ROOT=/var/lib/gridengine
+  - export SGE_CELL=default
+  - export DRMAA_LIBRARY_PATH=/usr/lib/libdrmaa.so.1.0
 install:
   # - conda create -n qiime_env python=2.7 qiime matplotlib=1.4.3 mock nose -c bioconda
   - conda create -n test_env python=$PYVERSION --file ci/conda_requirements.txt

travis/host_template

@@ -0,0 +1,9 @@
+hostname localhost
+load_scaling NONE
+complex_values NONE
+user_lists arusers
+xuser_lists NONE
+projects NONE
+xprojects NONE
+usage_scaling NONE
+report_variables NONE

travis/install_sge.sh

@@ -0,0 +1,29 @@
+#!/bin/bash
+# This script installs and configures a Sun Grid Engine installation for use
+# on a Travis instance.
+#
+# Written by Dan Blanchard ([email protected]), September 2013
+
+cd travis
+sudo sed -i -r "s/^(127.0.0.1\s)(localhost\.localdomain\slocalhost)/\1localhost localhost.localdomain $(hostname) /" /etc/hosts
+sudo apt-get update -qq
+echo "gridengine-master shared/gridenginemaster string localhost" | sudo debconf-set-selections
+echo "gridengine-master shared/gridenginecell string default" | sudo debconf-set-selections
+echo "gridengine-master shared/gridengineconfig boolean true" | sudo debconf-set-selections
+sudo apt-get install gridengine-common gridengine-master
+# Do this in a separate step to give master time to start
+sudo apt-get install libdrmaa1.0 gridengine-client gridengine-exec
+export CORES=$(grep -c '^processor' /proc/cpuinfo)
+sed -i -r "s/template/$USER/" user_template
+sudo qconf -Auser user_template
+sudo qconf -au $USER arusers
+sudo qconf -as localhost
+export LOCALHOST_IN_SEL=$(qconf -sel | grep -c 'localhost')
+if [ $LOCALHOST_IN_SEL != "1" ]; then sudo qconf -Ae host_template; else sudo qconf -Me host_template; fi
+sed -i -r "s/UNDEFINED/$CORES/" queue_template
+sudo qconf -Ap smp_template
+sudo qconf -Aq queue_template
+echo "Printing queue info to verify that things are working correctly."
+qstat -f -q all.q -explain a
+echo "You should see sge_execd and sge_qmaster running below:"
+ps aux | grep "sge"

travis/queue_template

@@ -0,0 +1,50 @@
+qname all.q
+hostlist localhost
+seq_no 0
+load_thresholds np_load_avg=1.75
+suspend_thresholds NONE
+nsuspend 1
+suspend_interval 00:05:00
+priority 0
+min_cpu_interval 00:05:00
+processors UNDEFINED
+qtype BATCH INTERACTIVE
+ckpt_list NONE
+pe_list make smp
+rerun FALSE
+slots UNDEFINED
+tmpdir /tmp
+shell /bin/bash
+prolog NONE
+epilog NONE
+shell_start_mode posix_compliant
+starter_method NONE
+suspend_method NONE
+resume_method NONE
+terminate_method NONE
+notify 00:00:60
+owner_list NONE
+user_lists arusers
+xuser_lists NONE
+subordinate_list NONE
+complex_values NONE
+projects NONE
+xprojects NONE
+calendar NONE
+initial_state default
+s_rt INFINITY
+h_rt INFINITY
+s_cpu INFINITY
+h_cpu INFINITY
+s_fsize INFINITY
+h_fsize INFINITY
+s_data INFINITY
+h_data INFINITY
+s_stack INFINITY
+h_stack INFINITY
+s_core INFINITY
+h_core INFINITY
+s_rss INFINITY
+h_rss INFINITY
+s_vmem INFINITY
+h_vmem INFINITY

travis/smp_template

@@ -0,0 +1,11 @@
+pe_name            smp
+slots              999
+user_lists         NONE
+xuser_lists        NONE
+start_proc_args    /bin/true
+stop_proc_args     /bin/true
+allocation_rule    $pe_slots
+control_slaves     FALSE
+job_is_first_task  TRUE
+urgency_slots      min
+accounting_summary FALSE

travis/user_template

@@ -0,0 +1,5 @@
+name template
+oticket 0
+fshare 0
+delete_time 0
+default_project NONE