[Scons-users] Trouble installing package on a supercomputer.

[Ray Sheppard]

Hi Jason,
   Thanks for the help.  I apologize I have tried to shorten my 
explanations to save space.  I know I am getting the mpicc wrapper from 
the OpenMPI build, I built it.  There is no Intel mpicc on the system.  
I (well actually Jim Dietz maintains the Intel compiler) did not install 
the Intel MPI package.  We spun off the compiler and I used that to 
build the MPI.  It is properly in my path and the build system sees and 
uses it.  It also goes off on its own to look for a license that does 
not exist. OpenMPI does not have one.  Somewhere, the system has been 
told that if it is going to use MPI, there is a license file needed.  I 
am sorry but it is wrong.  As with most software, it is fairly hard 
headed about it until I can find where it might think that.
   So, I decided that it might think differently about GNU.  I built an 
OpenMPI for GNU and swapped paths.  I did much better. It now assembles 
a compile line.  I have never been a fan of parallel compilations, so it 
likely has a long way to go, but the intermediate files are compiling as 
mpicc and mpiCC by telling scons.py cxx=gcc and extras=mpi,static.  
Thanks for the help, but if I can't turn off the license,  GNU will have 
to do.  The scary part is that I am just building on the cluster for 
practice.  The original request from the Cell and Virus Theory Center 
was to put this beast on the Cray.
                            Ray

On 9/10/2014 4:46 PM, Kenny, Jason L wrote:
>
> Hi,
>
> So there are a lot of details that go in to a MPI build. As I 
> understand it the Intel MPI is based on the MPICH as well. From what I 
> can pull out from the e-mail ( and note I am not a MPI/cluster expert 
> .. the team next to me is, so this is more their suggestion) is that 
> you probably are having a path issue at the moment. Since your are 
> pulling you shell path in to the scons build, you souls check to see 
> which mpicxx you are using. You have it hard coded in to replace the 
> cxx with mpicxx... This is just a general mpi compiler wrapper that is 
> not explicit to Intel or Cray versions of the compiler. It could call 
> anything depending on your current shell environment.
>
> So at the moment form what I understand of your setup, this is not as 
> much a scons issues but what tools are being called in the toolchain. 
> I am pretty sure given what you have shown so far, this would not be 
> any different using gmake.
>
> Jason
>
> *From:*Scons-users [mailto:scons-users-bounces at scons.org] *On Behalf 
> Of *Ray Sheppard
> *Sent:* Wednesday, September 10, 2014 3:11 PM
> *To:* SCons users mailing list
> *Subject:* Re: [Scons-users] Trouble installing package on a 
> supercomputer.
>
> Thanks,
>   The real problem is that there is no license file.  It keeps looking 
> for an Intel compiler license file but we do not use Intel MPI.  I do 
> have an Intel built OpenMPI on the cluster. So, I have tried to just 
> get that to build.  This package seems happier (less initial errors) 
> on the cluster than the originally requested Cray.  The package 
> understands and uses the proper mpicc/CC, but then expects it to be 
> Intel and need a license, which it isn't and doesn't.  I would love to 
> just turn that off somehow.
>
>  The Cray uses its own MPI, which is based on MPICH2. That has a 
> license associated with it, but it has larger issues.   The Cade 
> automatically searches for library calls in the source code and links 
> things like MPI and various math libraries without an external 
> compiler wrapper like mpicc or explicit links like -llapack. That 
> seemed to drive the build nuts in various ways.
>
> Thanks again for the help,
>    Ray
>
> On 9/10/2014 3:16 PM, Kenny, Jason L wrote:
>
>     HI,
>
>     Looks like you are using the MPI compiler. SCons ( and my
>     extension Parts) don't directly support the MPI compiler at the
>     moment via a tool. From what I see below it look like you the path
>     needed for the license to be seen by the compiler is missing.
>
>     There are two ways to fix this.
>
>     1)Add the intelc tool to the toolchain you are using. This should
>     setup the stuff needed to find the license file.
>
>     2)The script you would normally run to source the path to run this
>     compiler would add a variable INTEL_LICENSE_FILE to the shell
>     environment. If you take this value and add it to the env["EVV"]
>     value the compiler should work. Form below I think this added line
>     should work.
>
>             "overrides" : {
>                         "ENV" : {
>     "LIBRARY_PATH":os.environ["LIBRARY_PATH"],
>     "LD_LIBRARY_PATH":os.environ["LD_LIBRARY_PATH"],
>     "CPATH":os.environ["CPATH"],
>     "PATH":os.environ["PATH"],
>     "MODULEPATH":os.environ["MODULEPATH"],
>     "MODULESHOME":os.environ["MODULESHOME"],
>
>     *"INTEL_LICENSE_FILE":**os.environ[**"INTEL_LICENSE_FILE"**],**
>     *                }
>             },
>
>
>     Hope this helps
>
>     Jason
>
>

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