Question: How to Install SGE (Sun Grid Engine) on macOS Sierra?
2
gravatar for Deepak Tanwar
3.4 years ago by
Deepak Tanwar4.0k
ETH Zürich, Switzerland
Deepak Tanwar4.0k wrote:

This Question could be little offtrack. I am trying to install SGE on MacPro. This would be useful in scheduling NGS analysis.

I have tried a lot:

https://bioteam.net/2010/02/grid-engine-6-2-on-mac-os-x/

http://sparsefile.blogspot.ca/2012/06/installing-open-grid-scheduler-aka-sun.html

https://docs.oracle.com/cd/E19787-01/820-3702/6nf7ge6e0/index.html

After trying for 6 hours, finally asking Bioinformatics experts.

How can I install SGE on MacOS Sierra 10.12.3?

If I cannot, than is there an alternative for it?

macos sge • 3.0k views
ADD COMMENTlink modified 2.5 years ago by se3940 • written 3.4 years ago by Deepak Tanwar4.0k
1

Are you looking to simply launch scheduled jobs? You could do that following directions here.

Links you have in OP are from several years ago and it is not surprising that things are not working with the latest macOS.

ADD REPLYlink written 3.4 years ago by genomax87k
1

For alternatives, you can have a look at this page.

ADD REPLYlink modified 3.4 years ago • written 3.4 years ago by h.mon30k
1

I think that OGE/SGE is pretty much dead these days. But then I would question that you need it in the first place. Why do you need a cluster software for a single computer, it would be way oversized a solution.

ADD REPLYlink written 3.4 years ago by Michael Dondrup47k
2

Last update to Son of Grid Engine was 2016-03-02

ADD REPLYlink written 3.4 years ago by 5heikki8.9k
0
gravatar for se394
2.5 years ago by
se3940
se3940 wrote:

I was able to get this running on a 2013 mac pro. Currently working on adding 2010 mac pros as execution hosts. The compilation is pretty straight forward. The tricky part is configuring your network, setting the mac os application firewall and opening the right ports. Here are instructions for compilation.

The GE2011.11p1 distribution was downloaded from source forge: http://sourceforge.net/projects/gridscheduler/files and untar’d:

wget -O GE2011.11p1.tar.gz https://sourceforge.net/projects/gridscheduler/files/GE2011.11p1/GE2011.11p1.tar.gz/download
tar zvxf GE2011.11p1.tar

A few hacks were necessary to compile from source on mac OS High Sierra.

The authuser.c file in ./utilbin was edited to find the authentication software in OS X (pam_app.h). Line 70 was changed to /usr/include/security/pam_appl.h.

The final compilation step will not work since the source build was not configured for a modern mac OS install. You will need to install automake-1.15 and copy the config.guess and config.sub to the build directory. i.e.)

brew install automake

cp -v /usr/local/Cellar/automake/1.15.1/share/automake-1.15/config.guess 
/Volumes/Anvil/opt/GE2011.11p1/source/3rdparty/qtcsh/
cp -v /usr/local/Cellar/automake/1.15.1/share/automake-1.15/config.sub 
/Volumes/Anvil/opt/GE2011.11p1/source/3rdparty/qtcsh/

To compile:

cd ./GE2011.p1/source

./aimk -no-java -no-secure -spool-classic -no-dump -only-depend

./scripts/zerodepend

./aimk -no-java -no-secure -spool-classic -no-dump depend

./aimk -no-java -no-secure -spool-classic -no-dump

export SGE_ROOT=/Volumes/Anvil/opt/sge

mkdir $SGE_ROOT

scripts/distinst -all -local -noexit

cd $SGE_ROOT

Still working on getting java compiled.. but its really tough and I don't know java so hard for me to debug..

ADD COMMENTlink modified 2.5 years ago by genomax87k • written 2.5 years ago by se3940
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