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.p2.spkg
and drop it into spkg/standard - then run make again and the problem
should go away.
Cheers,
Michael
> real 10m29.755s
> user 9m17.776s
> sys 0m50.167s
> sage: An error occurred while installing atlas-3.8.p6
> 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/atlas-3.8.p6 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/atlas-3.8.p6
> (When you are done debugging, you can type "exit" to leave the
> subshell.)
> make[1]: *** [installed/atlas-3.8.p6] Error 1
> make[1]: Leaving directory `/data1/sources/sage-2.9.1.1/spkg'
>
> real 22m21.025s
> user 17m26.185s
> sys 3m11.789s
>
> So now it does not seem to find gfortran library:
> [EMAIL PROTECTED] sage-2.9.1.1]$ locate libgfortran
> /usr/lib/libgfortran.so.1
> /usr/lib/libgfortran.so.1.0.0
> /usr/lib/gcc/i386-redhat-linux/4.1.2/libgfortran.a
> /usr/lib/gcc/i386-redhat-linux/4.1.2/libgfortran.so
> /usr/lib/gcc/i386-redhat-linux/4.1.2/libgfortranbegin.a
> /usr/share/doc/gcc-gfortran-4.1.2/ChangeLog.libgfortran.bz2
>
> I assume that this is the real problem, and that the missing threaded
> ATLAS libraries are actually not a problem....
>
> On Jan 4, 11:22 am, Johannct <[EMAIL PROTECTED]> wrote:
>
> > I rebuilt in place, and I just realized that I might have issued the
> > command make -j2 the first time, as I have a dual core machine. So I
> > am just remaking with this command just to see..... If that fails I
> > will start from a fresh source again.....
>
> > On Jan 4, 11:18 am, mabshoff <[EMAIL PROTECTED]
>
> > dortmund.de> wrote:
> > > On Jan 4, 8:10 pm, Johannct <[EMAIL PROTECTED]> wrote:
>
> > > > ok, now it fails before numpy seemingly : it did not build all the
> > > > atlas librairies and bail out after complainng that it cannot cp
> > > > them... I relaunched a make, and it seems to build all the libs again,
> > > > which is strange...
> > > > Anyway :
> > > > 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
>
> > > > and indeed:
> > > > [EMAIL PROTECTED] sage-2.9.1.1]$ ls /data1/sources/sage-2.9.1.1/spkg/
> > > > build/atlas-3.8.p6/ATLAS-build/lib/
> > > > libatlas.a libatlas.so libcblas.a libcblas.so libclapack.a
> > > > libf77blas.a libf77blas.so liblapack.a liblapack.so libtstatlas.a
> > > > Makefile Make.inc
>
> > > That is to be expected. the libraries it complains about are the multi
> > > threaded versions of ATLAS which we do not build. If they do not exist
> > > the makefile from ATLAS just ignores those errors. Look in the spkg-
> > > install in spkg/build/atlas-3.8.p6/ to see what we do.
>
> > > One more question: did you start with a fresh build from vanilla
> > > sources or did you rebuild in place?
>
> > > Cheers,
>
> > > Michael
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