[Scons-users] Trouble installing package on a supercomputer.
Ray Sheppard
rsheppar at iu.edu
Wed Sep 10 16:11:10 EDT 2014
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
>
> *From:*Scons-users [mailto:scons-users-bounces at scons.org] *On Behalf
> Of *Gary Oberbrunner
> *Sent:* Wednesday, September 10, 2014 1:48 PM
> *To:* SCons users mailing list
> *Subject:* Re: [Scons-users] Trouble installing package on a
> supercomputer.
>
> Hi Ray; SCons itself shouldn't care about filesystems or licenses.
> Most probably whatever package you're trying to use SCons to build
> has set things up in a way that isn't working at your site.
>
> Your first error refers to a "site.settings" file; that's not part of
> SCons. It's probably part of the software you're trying to build.
> Your Environment() line looks fine to me.
>
> Your second error, Error: A license for CCompL is not available
> (-76,61026,2), is I think from the Intel compiler. Probably again
> your software has set itself up to build with the Intel compiler tool
> (which is shipped with SCons); you may need to set an env var
> (os.environ, or env['ENV']) to tell the compiler where your license
> is. I think that env var is documented in the Intel compiler
> installation docs.
>
> On Wed, Sep 10, 2014 at 2:36 PM, Ray Sheppard <rsheppar at iu.edu
> <mailto:rsheppar at iu.edu>> wrote:
>
>
> Hello,
> I am quite lost. If I sent this to the wrong place, I apologize.
> Please direct me to the correct address. SCons seems to
> believe that it has control of the various file systems and that
> everything is where it expects it should be. On a supercomputer, that
> is not the case. I gave up on the Cray entirely. Now I am just
> trying
> to build with Intel on a large cluster. Using your FAQ, I tried
> to tell
> it to import my environment with:
> env = Environment(ENV = {'PATH' : path})
>
> However, that returns:
> File "site.settings", line 23, in <module>
> NameError: name 'Environment' is not defined
> scons: done reading SConscript files.
>
> Maybe I should Environment predeclared somewhere else, but I did not
> see where that might be. Also related, the SCons system seems to look
> for licenses where none are needed (or exist).
>
> scons: Building targets ...
> mpiCC -o
> build/src/release/linux/2.6/64/x86/icc/13.1/mpi-static/apps/public/AbinitioRelax.o
> -c -Wp64 -wd279,2259,1682 -ip -O3 -Qoption,c,-ip_ninl_max_stats=500
> -Qoption,c,-ip_ninl_max_total_stats=5000 -DNDEBUG -DUSEMPI
> -DEXIT_THROWS_EXCEPTION -Isrc -Iexternal/include
> -Isrc/platform/linux/64/icc/13.1 -Isrc/platform/linux/64/icc
> -Isrc/platform/linux/64 -Isrc/platform/linux -Iexternal/boost_1_46_1
> -Iexternal/dbio -I/usr/include -I/usr/local/include
> src/apps/public/AbinitioRelax.cc
>
> Error: A license for CCompL is not available (-76,61026,2).
>
> License file(s) used were (in this order):...
>
> However, an interactive compile of that line works just fine. I found
> the Module keywords in the scinet settings, however, nothing seems to
> change its mind.
>
> My site settings have changed a lot in the past week. Currently it
> looks like this:
> import os
> ## env = Environment(ENV = os.environ)
> settings = {
> "site" : {
> "prepends" : {
> "program_path" : os.environ["PATH"].split(":"),
> # "include_path" : os.environ["INCLUDE"].split(":"),
> "library_path" : os.environ["LD_LIBRARY_PATH"].split(":"),
> },
> "appends" : {
> "defines" : ["EXIT_THROWS_EXCEPTION"],
> },
> "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"],
> }
> },
> "mpi" : {
> "overrides" : {
> "cxx" : "mpicxx"
> },
> },
>
> "removes" : {
> },
> },
> }
>
> Hopefully, y'all see something simple a newbie like me is missing.
> Does this system have a place where the package developers must put a
> target dependency file? If I could find it, I am beginning to think
> it would be easier to strip it out and just build the package with
> gmake.
> Thanks.
> Ray
>
>
> --
> Respectfully,
> Ray Sheppard
> RSheppar at iu.edu <mailto:RSheppar at iu.edu>
> http://rt.uits.iu.edu/systems/SciAPT
> 317-274-0016 <tel:317-274-0016>
>
> Principal Analyst
> Senior Technical Lead
> Scientific Applications and Performance Tuning
> Research Technologies
> University Information Technological Services
> IUPUI campus
> Indiana University
>
> My "pithy" saying: Science is the art of translating the world
> into language. Unfortunately, that language is mathematics.
> Bumper sticker wisdom: Make it idiot-proof and they will make a
> better idiot.
>
>
>
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>
>
>
> --
> Gary
>
>
>
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