On Jan 4, 10:14 pm, Johannct <[EMAIL PROTECTED]> wrote:
Hi, > hello, > having root priviledge I went ahead and did : ln -s /usr/lib/ > libgfortran.so.1 /usr/lib/libgfortran.so > It fixes the problem in the sense that I am now back to square one, > with the initial numpy build failure : Ok, but you also see if it works with the new fortran.spkg and without the link? I tested the new spkg in a Debian box, but libgfortran.so is in /usr/lib, so I am not 100% sure that it will work. But it should since the location of libgfortran.so on RedHat/FC is not in LD_LIBRARY_PATH per default. > running install > running build > running config_cc > unifing config_cc, config, build_clib, build_ext, build commands -- > compiler options > running config_fc > unifing config_fc, config, build_clib, build_ext, build commands -- > fcompiler options > running build_src > building py_modules sources > building extension "numpy.core.multiarray" sources > Generating build/src.linux-i686-2.5/numpy/core/config.h > error: don't know how to compile Fortran code on platform 'posix' with > 'gfortran' compiler. Supported compilers are: > intelem,absoft,compaq,ibm,sun,lahey,sage_fortran,pg,hpux,intele,gnu95,intelv,g95,compaqv,mips,vast,nag,none,intel,f,gnu,intelev) > Error building numpy. > Try setting SAGE_ATLAS to the directory that contains lib/libatlas.a ? > > real 0m0.966s > user 0m0.560s > sys 0m0.169s > sage: An error occurred while installing numpy-20071020-1.0.3.1.p3 > Please email sage-develhttp://groups.google.com/group/sage-devel > explaining the problem and send the relevant part of > of /data1/sources/sage-2.9.1.1/install.log. Describe your computer, > operating system, etc. > If you want to try to fix the problem, yourself *don't* just cd to > /data1/sources/sage-2.9.1.1/spkg/build/numpy-20071020-1.0.3.1.p3 and > type 'make'. > Instead type "/data1/sources/sage-2.9.1.1/sage -sh" > in order to set all environment variables correctly, then cd to > /data1/sources/sage-2.9.1.1/spkg/build/numpy-20071020-1.0.3.1.p3 > (When you are done debugging, you can type "exit" to leave the > subshell.) > make[1]: *** [installed/numpy-20071020-1.0.3.1.p3] Error 1 > make[1]: Leaving directory `/data1/sources/sage-2.9.1.1/spkg' > > So now that it agrees to pick up gfortran, as the fortran compiler, it > messes up the platform.... Yeah, that sucks. Any chance you can provide any of us with a shell to hunt this down? The current situation is like poking around in the dark with one arm tied behind your back ;) > best, > Johann > > On Jan 4, 1:06 pm, "William Stein" <[EMAIL PROTECTED]> wrote: > > > On Jan 4, 2008 12:58 PM, mabshoff > > > <[EMAIL PROTECTED]> wrote: > > > > On Jan 4, 9:52 pm, Johannct <[EMAIL PROTECTED]> wrote: > > > > fresh rebuild from a vanilla source, LD_LIBRARY_PATH, PYTHONPATH > > > > etc... unsetenved, and using make and *not* make -j2 and using > > > > SAGE_FORTRAN set to gfortran, I still stumble : > > > > > make[3]: `libcblas.so' is up to date. > > > > make[3]: Leaving directory `/data1/sources/sage-2.9.1.1/spkg/build/ > > > > atlas-3.8.p6/ATLAS-build/lib' > > > > make[2]: Leaving directory `/data1/sources/sage-2.9.1.1/spkg/build/ > > > > atlas-3.8.p6/ATLAS-build/lib' > > > > make[2]: Entering directory `/data1/sources/sage-2.9.1.1/spkg/build/ > > > > atlas-3.8.p6/ATLAS-build' > > > > mkdir -p /data1/sources/sage-2.9.1.1/local/include/atlas > > > > chmod 0755 /data1/sources/sage-2.9.1.1/local/include/atlas > > > > make -f Make.top install_inc INSTdir=/data1/sources/sage-2.9.1.1/local/ > > > > include > > > > make[3]: Entering directory `/data1/sources/sage-2.9.1.1/spkg/build/ > > > > atlas-3.8.p6/ATLAS-build' > > > > cp /data1/sources/sage-2.9.1.1/spkg/build/atlas-3.8.p6/ATLAS-build/../ > > > > src/ATLAS//include/cblas.h /data1/sources/sage-2.9.1.1/local/include/. > > > > cp /data1/sources/sage-2.9.1.1/spkg/build/atlas-3.8.p6/ATLAS-build/../ > > > > src/ATLAS//include/clapack.h /data1/sources/sage-2.9.1.1/local/ > > > > include/. > > > > chmod 0644 /data1/sources/sage-2.9.1.1/local/include/cblas.h /data1/ > > > > sources/sage-2.9.1.1/local/include/clapack.h > > > > cp /data1/sources/sage-2.9.1.1/spkg/build/atlas-3.8.p6/ATLAS-build/ > > > > include/* /data1/sources/sage-2.9.1.1/local/include/atlas/. > > > > chmod 0644 /data1/sources/sage-2.9.1.1/local/include/atlas/* > > > > make[3]: Leaving directory `/data1/sources/sage-2.9.1.1/spkg/build/ > > > > atlas-3.8.p6/ATLAS-build' > > > > make -f Make.top install_lib INSTdir=/data1/sources/sage-2.9.1.1/local/ > > > > lib > > > > make[3]: Entering directory `/data1/sources/sage-2.9.1.1/spkg/build/ > > > > atlas-3.8.p6/ATLAS-build' > > > > cp /data1/sources/sage-2.9.1.1/spkg/build/atlas-3.8.p6/ATLAS-build/lib/ > > > > libatlas.a /data1/sources/sage-2.9.1.1/local/lib/. > > > > cp /data1/sources/sage-2.9.1.1/spkg/build/atlas-3.8.p6/ATLAS-build/lib/ > > > > libcblas.a /data1/sources/sage-2.9.1.1/local/lib/. > > > > cp /data1/sources/sage-2.9.1.1/spkg/build/atlas-3.8.p6/ATLAS-build/lib/ > > > > liblapack.a /data1/sources/sage-2.9.1.1/local/lib/. > > > > chmod 0644 /data1/sources/sage-2.9.1.1/local/lib/libatlas.a /data1/ > > > > sources/sage-2.9.1.1/local/lib/liblapack.a \ > > > > /data1/sources/sage-2.9.1.1/local/lib/libcblas.a > > > > cp /data1/sources/sage-2.9.1.1/spkg/build/atlas-3.8.p6/ATLAS-build/lib/ > > > > libf77blas.a /data1/sources/sage-2.9.1.1/local/lib/. > > > > chmod 0644 /data1/sources/sage-2.9.1.1/local/lib/libf77blas.a > > > > cp /data1/sources/sage-2.9.1.1/spkg/build/atlas-3.8.p6/ATLAS-build/lib/ > > > > libptcblas.a /data1/sources/sage-2.9.1.1/local/lib/. > > > > cp: cannot stat `/data1/sources/sage-2.9.1.1/spkg/build/atlas-3.8.p6/ > > > > ATLAS-build/lib/libptcblas.a': No such file or directory > > > > make[3]: [install_lib] Error 1 (ignored) > > > > cp /data1/sources/sage-2.9.1.1/spkg/build/atlas-3.8.p6/ATLAS-build/lib/ > > > > libptf77blas.a /data1/sources/sage-2.9.1.1/local/lib/. > > > > cp: cannot stat `/data1/sources/sage-2.9.1.1/spkg/build/atlas-3.8.p6/ > > > > ATLAS-build/lib/libptf77blas.a': No such file or directory > > > > make[3]: [install_lib] Error 1 (ignored) > > > > chmod 0644 /data1/sources/sage-2.9.1.1/local/lib/libptcblas.a /data1/ > > > > sources/sage-2.9.1.1/local/lib/libptf77blas.a > > > > chmod: cannot access `/data1/sources/sage-2.9.1.1/local/lib/ > > > > libptcblas.a': No such file or directory > > > > chmod: cannot access `/data1/sources/sage-2.9.1.1/local/lib/ > > > > libptf77blas.a': No such file or directory > > > > make[3]: [install_lib] Error 1 (ignored) > > > > cp /data1/sources/sage-2.9.1.1/spkg/build/atlas-3.8.p6/ATLAS-build/lib/ > > > > libatlas.so /data1/sources/sage-2.9.1.1/local/lib/. > > > > cp /data1/sources/sage-2.9.1.1/spkg/build/atlas-3.8.p6/ATLAS-build/lib/ > > > > libcblas.so /data1/sources/sage-2.9.1.1/local/lib/. > > > > cp /data1/sources/sage-2.9.1.1/spkg/build/atlas-3.8.p6/ATLAS-build/lib/ > > > > libf77blas.so /data1/sources/sage-2.9.1.1/local/lib/. > > > > cp /data1/sources/sage-2.9.1.1/spkg/build/atlas-3.8.p6/ATLAS-build/lib/ > > > > liblapack.so /data1/sources/sage-2.9.1.1/local/lib/. > > > > chmod 0644 /data1/sources/sage-2.9.1.1/local/lib/libatlas.so /data1/ > > > > sources/sage-2.9.1.1/local/lib/liblapack.so \ > > > > /data1/sources/sage-2.9.1.1/local/lib/ > > > > libcblas.so /data1/sources/sage-2.9.1.1/local/lib/libcblas.so > > > > make[3]: Leaving directory `/data1/sources/sage-2.9.1.1/spkg/build/ > > > > atlas-3.8.p6/ATLAS-build' > > > > make[2]: Leaving directory `/data1/sources/sage-2.9.1.1/spkg/build/ > > > > atlas-3.8.p6/ATLAS-build' > > > > ld -L/data1/sources/sage-2.9.1.1/local/lib -shared -soname > > > > liblapack.so -o liblapack.so --whole-archive liblapack.a --no-whole- > > > > archive -lc -lm -lgfortran > > > > ld: cannot find -lgfortran > > > > ld -L/data1/sources/sage-2.9.1.1/local/lib -shared -soname > > > > libf77blas.so -o libf77blas.so --whole-archive libf77blas.a --no-whole- > > > > archive -lc -lm -lgfortran > > > > ld: cannot find -lgfortran > > > > Hi, > > > > that is a known bug that ought to be fixed in 2.9.2 (out in a couple > > > hours). You can download > > > >http://sage.math.washington.edu/home/jkantor/spkgs/fortran-20071120.p... > > > > and drop it into spkg/standard - then run make again and the problem > > > should go away. > > > I don't think the above spkg actually fixes the problem, as you'll > > probably find out > > if you try it. > > > Something that Kate suggested is to symlink: > > > /usr/lib/gcc/i386-redhat-linux/4.1.2/libgfortran.so to $SAGE_ROOT/local/lib/ I don't like that solution too much, but it seems to be like a last resort solution. It also requires that the user known where libgfortran.so is located since the location varies by distribution and even compiler release. Cheers, Michael > > i.e., cd to SAGE_ROOT/local/lib/ and type > > > ln - s /usr/lib/gcc/i386-redhat-linux/4.1.2/libgfortran.so . > > > Please report back if this does/doesn't work for you. It worked for Kate. > > > We are going to add an environement variable for 2.9.2 so the above symlink > > can be created automatically during the SAGE build. > > > Thanks! --~--~---------~--~----~------------~-------~--~----~ To post to this group, send email to sage-devel@googlegroups.com To unsubscribe from this group, send email to [EMAIL PROTECTED] For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://sage.scipy.org/sage/ and http://modular.math.washington.edu/sage/ -~----------~----~----~----~------~----~------~--~---
