Just a heads up, we don't have a huge amount of space on this machine, ~750 GB for the git repos. We can include some data in the projects, but really big datasets will need to remain elsewhere. For anyone new to Git, this is a fairly good place to start: http://gitref.org/index.html Documentation for Gitlab is available here: http://doc.gitlab.com/

Commit 9e471622 authored by Khalid Kunji's avatar Khalid Kunji

fixed bugs and added some refinements

parent d6492d02
......@@ -77,9 +77,9 @@ free_mem=$(free | grep "buffers/cache" | rev | cut -d" " -f1 | rev)
if [ ${verbose} ]
then
echo "Kernel: " $(uname -r)
echo $(uname -r) > kern_check
echo "2.6.24" >> kern_check
fi
echo $(uname -r) > kern_check
echo "2.6.24" >> kern_check
kern=$(sort -V kern_check | head -1)
if [ ${verbose} ]
then
......
......@@ -9,7 +9,10 @@ fi
mkdir -p "${output_folder}/${run_name}/LOGS"
echo "Logs in: " "${output_folder}/${run_name}/LOGS"
cd ${input_folder}
find "${gigi_split_prefix%/*}" -name "chunk_0*"
if [ ${verbose} ]
then
find "${gigi_split_prefix%/*}" -name "chunk_0*"
fi
if [[ -n $(find "${gigi_split_prefix%/*}" -name "chunk_0*") ]]
then
echo "chunk_0.geno exists, file is most likely already split, if it is not, then remove the existing chunks from ${gigi_split_prefix%/*} and try again"
......
......@@ -33,9 +33,33 @@ do
fi
if [[ "$long" == "true" ]]
then
cgexec -g memory,cpu:test/test_limits $timecmd -o "${output_folder}/${run_name}/STATS/time${BASH_REMATCH}.log" -f'memory in kilobytes %M real %e user %U sys %S command %C' "${gigi}" "${file}" -outD="${output_folder}/${run_name}/gigi_output/${BASH_REMATCH}" -long > "${output_folder}/${run_name}/LOGS/${BASH_REMATCH}.gigi.log" & pids+=("$!")
if [ ${memory} ]
then
command -v cgexec >/dev/null 2>&1
cgexecpresent=$?
if [ ${cgexecpresent} ]
then
cgexec -g memory,cpu:user_cgroup/gigi $timecmd -o "${output_folder}/${run_name}/STATS/time${BASH_REMATCH}.log" -f'memory in kilobytes %M real %e user %U sys %S command %C' "${gigi}" "${file}" -outD="${output_folder}/${run_name}/gigi_output/${BASH_REMATCH}" -long > "${output_folder}/${run_name}/LOGS/${BASH_REMATCH}.gigi.log" & pids+=("$!")
else
echo "Memory limit requested but cgexec from cgroup-tools/libcgroup is not installed, running without limits"
$timecmd -o "${output_folder}/${run_name}/STATS/time${BASH_REMATCH}.log" -f'memory in kilobytes %M real %e user %U sys %S command %C' "${gigi}" "${file}" -outD="${output_folder}/${run_name}/gigi_output/${BASH_REMATCH}" -long > "${output_folder}/${run_name}/LOGS/${BASH_REMATCH}.gigi.log" & pids+=("$!")
fi
else
$timecmd -o "${output_folder}/${run_name}/STATS/time${BASH_REMATCH}.log" -f'memory in kilobytes %M real %e user %U sys %S command %C' "${gigi}" "${file}" -outD="${output_folder}/${run_name}/gigi_output/${BASH_REMATCH}" -long > "${output_folder}/${run_name}/LOGS/${BASH_REMATCH}.gigi.log" & pids+=("$!")
fi
else
cgexec -g memory,cpu:test/test_limits $timecmd -o "${output_folder}/${run_name}/STATS/time${BASH_REMATCH}.log" -f'memory in kilobytes %M real %e user %U sys %S command %C' "${gigi}" "${file}" -outD="${output_folder}/${run_name}/gigi_output/${BASH_REMATCH}" > "${output_folder}/${run_name}/LOGS/${BASH_REMATCH}.gigi.log" & pids+=("$!")
if [ ${memory} ]
then
if [ ${cgexecpresent} ]
then
cgexec -g memory,cpu:user_cgroup/gigi $timecmd -o "${output_folder}/${run_name}/STATS/time${BASH_REMATCH}.log" -f'memory in kilobytes %M real %e user %U sys %S command %C' "${gigi}" "${file}" -outD="${output_folder}/${run_name}/gigi_output/${BASH_REMATCH}" > "${output_folder}/${run_name}/LOGS/${BASH_REMATCH}.gigi.log" & pids+=("$!")
else
echo "Memory limit requested but cgexec from cgroup-tools/libcgroup is not installed, running without limits"
$timecmd -o "${output_folder}/${run_name}/STATS/time${BASH_REMATCH}.log" -f'memory in kilobytes %M real %e user %U sys %S command %C' "${gigi}" "${file}" -outD="${output_folder}/${run_name}/gigi_output/${BASH_REMATCH}" > "${output_folder}/${run_name}/LOGS/${BASH_REMATCH}.gigi.log" & pids+=("$!")
fi
else
$timecmd -o "${output_folder}/${run_name}/STATS/time${BASH_REMATCH}.log" -f'memory in kilobytes %M real %e user %U sys %S command %C' "${gigi}" "${file}" -outD="${output_folder}/${run_name}/gigi_output/${BASH_REMATCH}" > "${output_folder}/${run_name}/LOGS/${BASH_REMATCH}.gigi.log" & pids+=("$!")
fi
fi
last_pid="$!"
echo "gigi pid: " "$last_pid" " for part: " "${BASH_REMATCH}"
......
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