Links to svn.broadinstitute.org not working

Hello all,

I am a systems administrator trying to install CellProfiler on our cluster. When I try to execute the Makefile which downloads CellProfiler’s dependencies, it will fail when trying to download “findlibjvm.class” because the server is not responsive. I did an nslookup on the server and tried pinging the IP from my desktop which also failed. Is the server svn.broadinstitute.org down? Am I doing something wrong? Any help is much appreciated.

Thanks,

Brian

Hi Brian,

Sorry for the slow response- hmm, no, I wasn’t aware of any downtime around then. Did the issue get resolved for you?

Regards,
David

Oh, but I should also say tangentially that the Linux Makefiles here are all quite old. It’s possible that they point to old repositories I suppose. Please see cellprofiler.org/linux.shtml for a more reliable method to install CellProfiler for CentOS, and you can also find some folks’ Docker solutions for other distros like Ubuntu by searching on the forum.

Hope that helps,
DAvid

Hi David,

Thank you for the reply. I am trying to install this application on our cluster and I need to install it using a different prefix. In our environment, we have a directory of tools that are mounted via NFS to our compute nodes. My strategy for installing this was to download the RPM files via yum and do an RPM install under a different prefix for the relocatable packages and install all the non-relocatable ones on the image of our compute nodes. I have not been able to get it working. Could you please point me in the right direction for installing this application on a cluster from source? Your help is much appreciated.

Thanks,

Brian

Hi Brian, coincidentally, I’m working on updating that script right now. There are still a couple glitches that cause a couple of unit tests to fail, but I think the tests are failing because of a problem on the machine I’m using to build it. I can’t check it in yet (probably will have to wait for the end of this week) but I can send you what I have got which should work for Red Hat 6. I haven’t done a clean build on what I have yet, but it is likely to work.

You can email me (leek@broadinstitute.org) and I’ll send you the makefile back or you can wait until I check in the version that’s tested and validated next week. It would be helpful to know which distro you’re building for so I can replicate if you have problems with the makefile.

–Lee

Hi,

I’m also trying to install cellprofiler on an HPC cluster and the svn.broadinstitute.org downloads during the build process don’t work. I guess it’s not accessible to the outside world?.

Was there a resolution for this issue? I grabbed release_2.1.1 source from github, which appears to be from July. Were the mentioned makefile fixes pushed after that?

Many Thanks,

DT