On Thu, Sep 8, 2011 at 3:06 AM, Tzanko Matev <[email protected]> wrote:
> Hello,
>
> The title says it all. I am trying to build and run SAGE on a cluster
> where I do not have root access. Unfortunately the only Fortran
> compiler there is ifort. I tried to compile my own custom GCC
> distribution and build SAGE with it, however this doesn't work, since
> the shared libraries of my GCC cannot be found at execution time.
If you set things up correctly, then including your own GCC has been
reported to work. You would have to include
the shared libraries in $SAGE_ROOT/local/lib/.
> The
> build process fails when compiling lapack.
When using your own GCC? So, the problem is that your GCC doesn't work?
> I tried adding the path to
> my libraries to the LD_LIBRARY_PATH environment variable, but this
> variable seems to be ignored by the system. All of my problems could
> be easily solved if it was possible to compile SAGE with static
> libraries.
That is not advisable. Python by default dynamically loads extension
modules at runtime.
In theory its possible to build Python with a certain set of extension
modules statically linked in,
but nobody has ever done this for all of Sage, and I would be very
surprised if it were even possible.
> On a related note, how to make sure that SAGE is using my own GCC and
> not the one provided by the system? What I did was simply to append
> the directory my_gcc/bin at the beginning of the PATH environment
> variable, but I am not sure if this is the right way to do it.
For better or worse, adjusting your PATH is currently the best way to
specify which GCC is used.
> Any advice would be greatly appreciated.
>
> Here is the relevant part from install.log:
>
>> make[1]: Entering directory `/stoll/btm212/sage/sage-4.7.1b/spkg'
>> /stoll/btm212/sage/sage-4.7.1b/spkg/pipestatus "sage-spkg ${SAGE_SPKG_OPTS}
>> lapack-20071123.p2 2>&1" "tee -a /stoll/btm212/sage/
>> sage-4.7.1b/spkg/logs/lapack-20071123.p2.log"
>> Warning: Attempted to overwrite SAGE_ROOT environment variable
>> lapack-20071123.p2
>> Machine:
>> Linux btrzx5-1 2.6.16.60-0.21-smp #1 SMP Tue May 6 12:41:02 UTC 2008 x86_64
>> x86_64 x86_64 GNU/Linux
>> Deleting directories from past builds of previous/current versions of
>> lapack-20071123.p2
>> Extracting package
>> /stoll/btm212/sage/sage-4.7.1b/spkg/standard/lapack-20071123.p2.spkg ...
>> -rw-r--r-- 1 btm212 bt_m2 3423099 2011-09-06 17:03
>> /stoll/btm212/sage/sage-4.7.1b/spkg/standard/lapack-20071123.p2.spkg
>> Finished extraction
>> ****************************************************
>> Host system
>> uname -a:
>> Linux btrzx5-1 2.6.16.60-0.21-smp #1 SMP Tue May 6 12:41:02 UTC 2008 x86_64
>> x86_64 x86_64 GNU/Linux
>> ****************************************************
>> ****************************************************
>> CC Version
>> gcc -v
>> Using built-in specs.
>> Target: x86_64-suse-linux
>> Configured with: ../configure --enable-threads=posix --prefix=/usr
>> --with-local-prefix=/usr/local --infodir=/usr/share/info --ma
>> ndir=/usr/share/man --libdir=/usr/lib64 --libexecdir=/usr/lib64
>> --enable-languages=c,c++,objc,fortran,obj-c++,java,ada --enable-
>> checking=release --with-gxx-include-dir=/usr/include/c++/4.1.2 --enable-ssp
>> --disable-libssp --disable-libgcj --with-slibdir=/li
>> b64 --with-system-zlib --enable-shared --enable-__cxa_atexit
>> --enable-libstdcxx-allocator=new --program-suffix= --enable-version
>> -specific-runtime-libs --without-system-libunwind --with-cpu=generic
>> --host=x86_64-suse-linux
>> Thread model: posix
>> gcc version 4.1.2 20070115 (SUSE Linux)
>> ****************************************************
>> make[2]: Entering directory
>> `/stoll/btm212/sage/sage-4.7.1b/spkg/build/lapack-20071123.p2/src'
>> ( cd INSTALL; make; ./testlsame; ./testslamch; \
>> ./testdlamch; ./testsecond; ./testdsecnd; ./testversion )
>> make[3]: Entering directory
>> `/stoll/btm212/sage/sage-4.7.1b/spkg/build/lapack-20071123.p2/src/INSTALL'
>> sage_fortran -fPIC -c lsame.f -o lsame.o
>> sage_fortran -fPIC -c lsametst.f -o lsametst.o
>> sage_fortran -o testlsame lsame.o lsametst.o
>> sage_fortran -fPIC -c slamch.f -o slamch.o
>> sage_fortran -fPIC -c slamchtst.f -o slamchtst.o
>> sage_fortran -o testslamch slamch.o lsame.o slamchtst.o
>> sage_fortran -fPIC -c dlamch.f -o dlamch.o
>> sage_fortran -fPIC -c dlamchtst.f -o dlamchtst.o
>> sage_fortran -o testdlamch dlamch.o lsame.o dlamchtst.o
>> sage_fortran -fPIC -c second_INT_CPU_TIME.f -o second_INT_CPU_TIME.o
>> sage_fortran -fPIC -c secondtst.f -o secondtst.o
>> [INFO] : TIMER value: INT_CPU_TIME (given by make.inc)
>> sage_fortran -o testsecond second_INT_CPU_TIME.o secondtst.o
>> sage_fortran -fPIC -c dsecnd_INT_CPU_TIME.f -o dsecnd_INT_CPU_TIME.o
>> sage_fortran -fPIC -c dsecndtst.f -o dsecndtst.o
>> [INFO] : TIMER value: INT_CPU_TIME (given by make.inc)
>> sage_fortran -o testdsecnd dsecnd_INT_CPU_TIME.o dsecndtst.o
>> sage_fortran -fPIC -c tstiee.f -o tstiee.o
>> sage_fortran -o testieee tstiee.o
>> sage_fortran -fPIC -c ilaver.f -o ilaver.o
>> sage_fortran -fPIC -c LAPACK_version.f -o LAPACK_version.o
>> sage_fortran -o testversion ilaver.o LAPACK_version.o
>> make[3]: Leaving directory
>> `/stoll/btm212/sage/sage-4.7.1b/spkg/build/lapack-20071123.p2/src/INSTALL'
>> ./testlsame: error while loading shared libraries: libgfortran.so.3: cannot
>> open shared object file: No such file or directory
>> ./testslamch: error while loading shared libraries: libgfortran.so.3: cannot
>> open shared object file: No such file or directory
>> ./testdlamch: error while loading shared libraries: libgfortran.so.3: cannot
>> open shared object file: No such file or directory
>> ./testsecond: error while loading shared libraries: libgfortran.so.3: cannot
>> open shared object file: No such file or directory
>> ./testdsecnd: error while loading shared libraries: libgfortran.so.3: cannot
>> open shared object file: No such file or directory
>> ./testversion: error while loading shared libraries: libgfortran.so.3:
>> cannot open shared object file: No such file or directory
>> make[2]: *** [lapack_install] Error 127
>> make[2]: Leaving directory
>> `/stoll/btm212/sage/sage-4.7.1b/spkg/build/lapack-20071123.p2/src'
>> Error compiling lapack.
You might copy libgfortran.so.3 into SAGE_ROOT/local/lib/.
>>
>> real 0m0.685s
>> user 0m0.400s
>> sys 0m0.184s
>> sage: An error occurred while installing lapack-20071123.p2
>> Please email sage-devel http://groups.google.com/group/sage-devel
>> explaining the problem and send the relevant part of
>> of /stoll/btm212/sage/sage-4.7.1b/install.log. Describe your computer,
>> operating system, etc.
>> If you want to try to fix the problem yourself, *don't* just cd to
>> /stoll/btm212/sage/sage-4.7.1b/spkg/build/lapack-20071123.p2 and type 'make
>> check' or whatever is appropriate.
>> Instead, the following commands setup all environment variables
>> correctly and load a subshell for you to debug the error:
>> (cd '/stoll/btm212/sage/sage-4.7.1b/spkg/build/lapack-20071123.p2' &&
>> '/stoll/btm212/sage/sage-4.7.1b/sage' -sh)
>> When you are done debugging, you can type "exit" to leave the
>> subshell.
>> make[1]: *** [installed/lapack-20071123.p2] Error 1
>> make[1]: Leaving directory `/stoll/btm212/sage/sage-4.7.1b/spkg'
>>
>> real 0m16.546s
>> user 0m2.660s
>> sys 0m0.716s
>> Error building Sage.
>
> Best regards,
> Tzanko Matev
>
> --
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>
--
William Stein
Professor of Mathematics
University of Washington
http://wstein.org
--
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