Re: [IMP-dev] problem running jobs on the cluster

[Daniel Russel <>]

It might make sense to set up a ccache for the cluster, like we have for the lab. The old netapp seems like a good place. That way only the first person has to wait around while a new checkout is being built. And we can provide some standard config.py files to make everything just work. Make sense?


On Sep 21, 2011, at 2:19 PM, Dave Barkan wrote:

> I was able to successfully build IMP on the cluster in fast mode. Right 
> now, I believe IMP is built daily in release mode on /diva1 for people 
> to use, but not in fast. Until we have something automated for that I 
> think people are doing it on their own.
> 
> The only thing that gave me trouble was the hdf5 stuff, which I 
> corrected by adding Daniel's hdf5 into my config file:
> 
> libpath="/netapp/sali/drussel/production/hdf5/lib"
> cxxflags="-m64 -mmmx -msse -msse2 -isystem 
> /netapp/sali/drussel/production/hdf5/include"
> 
> (I'm actually not sure if I needed both those lines or just one).
> 
> I asked Josh about updating hdf5 to version 1.8 on the cluster and he 
> said that there will soon be a major OS change and he'll do it after 
> that. For now it had dependencies which probably need to be updated 
> before hdf5 itself, and unless it's a priority, he'll wait until after 
> the OS change and do it all at once.
> 
> Maybe this is obvious to people, but since I had to ask around, here is 
> what I did to build IMP-fast, maybe it will be useful for others:
> 1. Check out IMP on the head node (the svn repository is accessible from 
> there)
> 2. Update the config file to include Daniel's hdf5 stuff (also he has 
> links to bullet and CGAL if you need those)
> 3. login to an interactive node and build there to avoid abusing the 
> head node. Since the disks are the same on the interactive node and the 
> head node, you can build on one and have it available on the other one.
> 
> Thanks to Dr. Rogers for helping me out with this.
> 
> db
> 
> 
> 
> On 9/21/11 7:37 AM, Daniel Russel wrote:
>> On Sep 21, 2011, at 6:18 AM, Keren Lasker wrote:
>> 
>> 
>>> thanks.
>>> so how do you think others are running things on the cluster these days? :)
>>> is everyone using your production version or installed things locally?
>>> 
>> I know of various combinations of using mine, using others, Charles was going to ask Josh to update some build machines or not using it at all. I like my production setup since you know there are no other libraries that are non-standard that are required. And I intent to keep things stable (most of the libraries there have version numbers in their paths).
>> 
>> 
>>> also, you can answer to that offline if more appropriate, but how do one link your hdf5 version with imp? is there a flag in the config file or something like that?
>>> 
>> As with all dependencies, just make sure the includepath, libpath, and perhaps, ldlibpath includes the library.
>> 
>> 
>>> On Sep 21, 2011, at 4:16 PM, Daniel Russel wrote:
>>> 
>>> 
>>>> I don't think hdf5 or at least appropriate versions of hdf5 is installed on the cluster as a whole. I suggest building against the version in ~drussel/production/hdf5 (you can copy that to your home dir if you want).
>>>> 
>>>> On Sep 21, 2011, at 3:41 AM, Keren Lasker wrote:
>>>> 
>>>> 
>>>>> hi:
>>>>> running jobs on our shared cluster i am getting an error:
>>>>> "ImportError: libhdf5.so.6: cannot open shared object file: No such file or directory"
>>>>> things are running ok on baton2, the problem occurs on the nodes of the cluster.
>>>>> any idea how to resolve that?
>>>>> 
>>>>> thanks, keren.
>>>>> _______________________________________________
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>>>>> 
>>>>> https://salilab.org/mailman/listinfo/imp-dev
>>>>> 
>>>> 
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