Re: [gentoo-user] Problem with cblas libraries
Thanks to all that responded. I've tried revdep-rebuild emerge --depclean revdep-rebuild with no progress on the errors I have. I've unmerged cblas* blas* gsl, synced, and emerge -uDN world also without success (also tried cblas-external USE flag but could not see it with eix). eselect cblas also gave no results. One problem I may have is with eselect. eselect-cblas has been unmerged but trying to re-emerge it gives this block. emerge -vp eselect-cblas These are the packages that would be merged, in order: Calculating dependencies... done! [ebuild N ] app-admin/eselect-cblas-0.1 0 kB [blocks B ] app-admin/eselect-cblas (app-admin/eselect-cblas is blocking sci-libs/lapack-reference-3.3.1-r1, sci-libs/gsl-1.15-r1) Total: 1 package (1 new), Size of downloads: 0 kB Conflict: 1 block (1 unsatisfied) * Error: The above package list contains packages which cannot be * installed at the same time on the same system. (app-admin/eselect-cblas-0.1::gentoo, ebuild scheduled for merge) pulled in by eselect-cblas (sci-libs/lapack-reference-3.3.1-r1::science, installed) pulled in by =sci-libs/lapack-reference-3.3 required by (virtual/lapack-3.3::science, installed) (sci-libs/gsl-1.15-r1::science, installed) pulled in by sci-libs/gsl required by (media-gfx/inkscape-0.48.2::gentoo, installed) =sci-libs/gsl-1.14-r2 required by (virtual/cblas-2.0::science, installed) For more information about Blocked Packages, please refer to the following section of the Gentoo Linux x86 Handbook (architecture is irrelevant): http://www.gentoo.org/doc/en/handbook/handbook-x86.xml?full=1#blocked Similar problem with eselect-blas and eselect-lapack. Any ideas before I try some more unmerging? Thanks Denis On Sat, Aug 27, 2011 at 18:34, Michael Mol mike...@gmail.com wrote: On Sat, Aug 27, 2011 at 11:27 AM, Valmor de Almeida val.gen...@gmail.com wrote: On 08/26/2011 08:12 AM, denis cohen wrote: Hello, I recently removed some packages like blas-reference, cblas-reference, and lapack-reference to get emerge to run (some blocking issues). Not sure that was a good idea because now, even if I've reinstalled these packages, I am having several new problems: [snip] Does anyone have an idea of how solve this problem? I'd be glad to provide more details. Thanks Denis Hi Denis, Have you done revdep-rebuild ? followed by a emerge --depclean ? before doing anything else after you removed the blas/lapack packages? revdep-rebuild emerge --depclean revdep-rebuild # Since emerge --depclean will warn that you should do a revdep-rebuild after it. -- :wq
Re: [gentoo-user] Problem with cblas libraries
On Tue, Aug 30, 2011 at 6:15 PM, denis cohen denis.co...@gmail.com wrote: Thanks to all that responded. I've tried revdep-rebuild emerge --depclean revdep-rebuild with no progress on the errors I have. I've unmerged cblas* blas* gsl, synced, and emerge -uDN world also without success (also tried cblas-external USE flag but could not see it with eix). eselect cblas also gave no results. One problem I may have is with eselect. eselect-cblas has been unmerged but trying to re-emerge it gives this block. emerge -vp eselect-cblas These are the packages that would be merged, in order: Calculating dependencies... done! [ebuild N ] app-admin/eselect-cblas-0.1 0 kB [blocks B ] app-admin/eselect-cblas (app-admin/eselect-cblas is blocking sci-libs/lapack-reference-3.3.1-r1, sci-libs/gsl-1.15-r1) Total: 1 package (1 new), Size of downloads: 0 kB Conflict: 1 block (1 unsatisfied) * Error: The above package list contains packages which cannot be * installed at the same time on the same system. (app-admin/eselect-cblas-0.1::gentoo, ebuild scheduled for merge) pulled in by eselect-cblas (sci-libs/lapack-reference-3.3.1-r1::science, installed) pulled in by =sci-libs/lapack-reference-3.3 required by (virtual/lapack-3.3::science, installed) (sci-libs/gsl-1.15-r1::science, installed) pulled in by sci-libs/gsl required by (media-gfx/inkscape-0.48.2::gentoo, installed) =sci-libs/gsl-1.14-r2 required by (virtual/cblas-2.0::science, installed) For more information about Blocked Packages, please refer to the following section of the Gentoo Linux x86 Handbook (architecture is irrelevant): http://www.gentoo.org/doc/en/handbook/handbook-x86.xml?full=1#blocked Similar problem with eselect-blas and eselect-lapack. Any ideas before I try some more unmerging? Are there newer versions of cblas, lapack-reference and gsl which you could unmask and update to? Grasping at straws, but maybe the block is caused by a of particular set of versions? -- :wq
Re: [gentoo-user] Problem with cblas libraries
denis cohen writes: I've unmerged cblas* blas* gsl, synced, and emerge -uDN world also without success (also tried cblas-external USE flag but could not see it with eix). What's your problem with the world update? Adding --tree to the emerge command might show what pulls in what. I had to unmerge clapack and lapack- reference yesterday, but I cannot remember the details - it all started with digikam not building because some blas stuff was missing. But finally the @world update was possible. And both got re-installed. eselect cblas also gave no results. Here it is set to the only option gsl. One problem I may have is with eselect. eselect-cblas has been unmerged but trying to re-emerge it gives this block. I get the very same blocker as you. eselect cblas is working, though. So is eselect-cblas being needed at all? Wonko
Re: [gentoo-user] Problem with cblas libraries
Following Michael Mol's advice I masked these in /etc/portage/package.mask: =virtual/blas-2.0 =virtual/cblas-2.0 =virtual/lapack-3.1 =sci-libs/cblas-reference-20030223-r5 =sci-libs/lapack-reference-3.2.1 =sci-libs/gsl-1.14 and did an emerge -uD world. All blocks were gone and after the emerge I got gsl working again. I am also not sure what use is eselect-cblas since eselect blas works without it. gmsh still won't emerge with these types of errors: ... [100%] Building CXX object CMakeFiles/gmsh.dir/contrib/bamg/bamglib/Meshio.cpp.o [100%] Building CXX object CMakeFiles/gmsh.dir/contrib/bamg/bamglib/QuadTree.cpp.o [100%] Building CXX object CMakeFiles/gmsh.dir/contrib/bamg/bamglib/SetOfE4.cpp.o Linking CXX executable gmsh CMakeFiles/gmsh.dir/Numeric/fullMatrix.cpp.o: In function `fullMatrixdouble::invertInPlace()': fullMatrix.cpp:(.text+0xcc): undefined reference to `dgesv_' CMakeFiles/gmsh.dir/Numeric/fullMatrix.cpp.o: In function `fullMatrixdouble::gemm(fullMatrixdouble const, fullMatrixdouble const, double, double)': fullMatrix.cpp:(.text+0x1e9): undefined reference to `dgemm_' CMakeFiles/gmsh.dir/Numeric/fullMatrix.cpp.o: In function `fullVectordouble::axpy(fullVectordouble const, double)': fullMatrix.cpp:(.text+0x260): undefined reference to `daxpy_' ... So making some progress. Denis On Wed, Aug 31, 2011 at 01:02, Alex Schuster wo...@wonkology.org wrote: denis cohen writes: I've unmerged cblas* blas* gsl, synced, and emerge -uDN world also without success (also tried cblas-external USE flag but could not see it with eix). What's your problem with the world update? Adding --tree to the emerge command might show what pulls in what. I had to unmerge clapack and lapack- reference yesterday, but I cannot remember the details - it all started with digikam not building because some blas stuff was missing. But finally the @world update was possible. And both got re-installed. eselect cblas also gave no results. Here it is set to the only option gsl. One problem I may have is with eselect. eselect-cblas has been unmerged but trying to re-emerge it gives this block. I get the very same blocker as you. eselect cblas is working, though. So is eselect-cblas being needed at all? Wonko
Re: [gentoo-user] Problem with cblas libraries
Just an update: gmsh build with USE=-blas Denis On Wed, Aug 31, 2011 at 01:14, denis cohen denis.co...@gmail.com wrote: Following Michael Mol's advice I masked these in /etc/portage/package.mask: =virtual/blas-2.0 =virtual/cblas-2.0 =virtual/lapack-3.1 =sci-libs/cblas-reference-20030223-r5 =sci-libs/lapack-reference-3.2.1 =sci-libs/gsl-1.14 and did an emerge -uD world. All blocks were gone and after the emerge I got gsl working again. I am also not sure what use is eselect-cblas since eselect blas works without it. gmsh still won't emerge with these types of errors: ... [100%] Building CXX object CMakeFiles/gmsh.dir/contrib/bamg/bamglib/Meshio.cpp.o [100%] Building CXX object CMakeFiles/gmsh.dir/contrib/bamg/bamglib/QuadTree.cpp.o [100%] Building CXX object CMakeFiles/gmsh.dir/contrib/bamg/bamglib/SetOfE4.cpp.o Linking CXX executable gmsh CMakeFiles/gmsh.dir/Numeric/fullMatrix.cpp.o: In function `fullMatrixdouble::invertInPlace()': fullMatrix.cpp:(.text+0xcc): undefined reference to `dgesv_' CMakeFiles/gmsh.dir/Numeric/fullMatrix.cpp.o: In function `fullMatrixdouble::gemm(fullMatrixdouble const, fullMatrixdouble const, double, double)': fullMatrix.cpp:(.text+0x1e9): undefined reference to `dgemm_' CMakeFiles/gmsh.dir/Numeric/fullMatrix.cpp.o: In function `fullVectordouble::axpy(fullVectordouble const, double)': fullMatrix.cpp:(.text+0x260): undefined reference to `daxpy_' ... So making some progress. Denis On Wed, Aug 31, 2011 at 01:02, Alex Schuster wo...@wonkology.org wrote: denis cohen writes: I've unmerged cblas* blas* gsl, synced, and emerge -uDN world also without success (also tried cblas-external USE flag but could not see it with eix). What's your problem with the world update? Adding --tree to the emerge command might show what pulls in what. I had to unmerge clapack and lapack- reference yesterday, but I cannot remember the details - it all started with digikam not building because some blas stuff was missing. But finally the @world update was possible. And both got re-installed. eselect cblas also gave no results. Here it is set to the only option gsl. One problem I may have is with eselect. eselect-cblas has been unmerged but trying to re-emerge it gives this block. I get the very same blocker as you. eselect cblas is working, though. So is eselect-cblas being needed at all? Wonko
Re: [gentoo-user] Problem with cblas libraries
On 08/26/2011 08:12 AM, denis cohen wrote: Hello, I recently removed some packages like blas-reference, cblas-reference, and lapack-reference to get emerge to run (some blocking issues). Not sure that was a good idea because now, even if I've reinstalled these packages, I am having several new problems: [snip] Does anyone have an idea of how solve this problem? I'd be glad to provide more details. Thanks Denis Hi Denis, Have you done revdep-rebuild ? followed by a emerge --depclean ? before doing anything else after you removed the blas/lapack packages? -- Valmor
Re: [gentoo-user] Problem with cblas libraries
On Sat, Aug 27, 2011 at 11:27 AM, Valmor de Almeida val.gen...@gmail.com wrote: On 08/26/2011 08:12 AM, denis cohen wrote: Hello, I recently removed some packages like blas-reference, cblas-reference, and lapack-reference to get emerge to run (some blocking issues). Not sure that was a good idea because now, even if I've reinstalled these packages, I am having several new problems: [snip] Does anyone have an idea of how solve this problem? I'd be glad to provide more details. Thanks Denis Hi Denis, Have you done revdep-rebuild ? followed by a emerge --depclean ? before doing anything else after you removed the blas/lapack packages? revdep-rebuild emerge --depclean revdep-rebuild # Since emerge --depclean will warn that you should do a revdep-rebuild after it. -- :wq
[gentoo-user] Problem with cblas libraries
Hello, I recently removed some packages like blas-reference, cblas-reference, and lapack-reference to get emerge to run (some blocking issues). Not sure that was a good idea because now, even if I've reinstalled these packages, I am having several new problems: - compiling gcc with the gsl library spits out errors like: g++ -L/usr/local/lib -lm -lgsl exact.o /usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/../../../../lib64/libgsl.so: undefined reference to `cblas_ctrmv' /usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/../../../../lib64/libgsl.so: undefined reference to `cblas_zswap' /usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/../../../../lib64/libgsl.so: undefined reference to `cblas_zsymm' /usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/../../../../lib64/libgsl.so: undefined reference to `cblas_cgeru' /usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/../../../../lib64/libgsl.so: undefined reference to `cblas_sgemm' /usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/../../../../lib64/libgsl.so: undefined reference to `cblas_ctrsv' /usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/../../../../lib64/libgsl.so: undefined reference to `cblas_sgemv' and so on... - still can't re-emerge packages like gsl and gmsh. For example, for gmsh I get; . [100%] Building CXX object CMakeFiles/gmsh.dir/contrib/bamg/bamglib/MeshDraw.cpp.o [100%] Building CXX object CMakeFiles/gmsh.dir/contrib/bamg/bamglib/MeshQuad.cpp.o [100%] Building CXX object CMakeFiles/gmsh.dir/contrib/bamg/bamglib/MeshWrite.cpp.o [100%] Building CXX object CMakeFiles/gmsh.dir/contrib/bamg/bamglib/Meshio.cpp.o [100%] Building CXX object CMakeFiles/gmsh.dir/contrib/bamg/bamglib/QuadTree.cpp.o make[2]: *** No rule to make target `/usr/lib64/libcblas.so', needed by `gmsh'. Stop. make[2]: *** Waiting for unfinished jobs [100%] Building CXX object CMakeFiles/gmsh.dir/contrib/bamg/bamglib/SetOfE4.cpp.o make[1]: *** [CMakeFiles/gmsh.dir/all] Error 2 make: *** [all] Error 2 emake failed * ERROR: sci-libs/gmsh-2.5.0 failed (compile phase): * Make failed! * * Call stack: * ebuild.sh, line 56: Called src_compile * environment, line 2995: Called cmake-utils_src_compile * environment, line 866: Called _execute_optionaly 'src_compile' * environment, line 291: Called enable_cmake-utils_src_compile * environment, line 1105: Called cmake-utils_src_make * environment, line 885: Called die * The specific snippet of code: * emake $@ || die Make failed!; * * If you need support, post the output of 'emerge --info =sci-libs/gmsh-2.5.0', * the complete build log and the output of 'emerge -pqv =sci-libs/gmsh-2.5.0'. * This ebuild is from an overlay named 'science': '/var/lib/layman/science/' * The complete build log is located at '/var/tmp/portage/sci-libs/gmsh-2.5.0/temp/build.log'. * The ebuild environment file is located at '/var/tmp/portage/sci-libs/gmsh-2.5.0/temp/environment'. * S: '/var/tmp/portage/sci-libs/gmsh-2.5.0/work/gmsh-2.5.0-source' Failed to emerge sci-libs/gmsh-2.5.0, Log file: '/var/tmp/portage/sci-libs/gmsh-2.5.0/temp/build.log' /usr/lib64/libcblas.so is present: Does anyone have an idea of how solve this problem? I'd be glad to provide more details. Thanks Denis
Re: [gentoo-user] Problem with cblas libraries
On 08/26/2011 02:12:35 PM, denis cohen wrote: Hello, I recently removed some packages like blas-reference, cblas- reference, and lapack-reference to get emerge to run (some blocking issues). Not sure that was a good idea because now, even if I've reinstalled these packages, I cannot say anything about sci-libs/gmsh since this is not in my portage tree. Are you using an overlay for that? As gsl is concerned I have sci-libs/gsl with the -cblas-external USE flag here. Helmut.
Re: [gentoo-user] Problem with cblas libraries
denis cohen writes:
I recently removed some packages like blas-reference, cblas-reference,
and lapack-reference to get emerge to run (some blocking issues).
I unmerged eselect-cblas and eselect-blas when I had similar problems, and I
think also {blas,cblas}-reference. The eselect packages got remerged
automatically, and some block I do not remember remained, but after some
days, a deep world update finally was working again.
Not sure that was a good idea because now, even if I've reinstalled
these packages,
I am having several new problems:
- compiling gcc with the gsl library spits out errors like:
g++ -L/usr/local/lib -lm -lgsl exact.o
/usr/lib/gcc/x86_64-pc-linux-gnu/4.5.3/../../../../lib64/libgsl.so:
undefined reference to `cblas_ctrmv'
[...]
and so on...
- still can't re-emerge packages like gsl and gmsh. For example, for gmsh
I get; .
[100%] Building CXX object
CMakeFiles/gmsh.dir/contrib/bamg/bamglib/MeshDraw.cpp.o
[100%] Building CXX object
CMakeFiles/gmsh.dir/contrib/bamg/bamglib/MeshQuad.cpp.o
[100%] Building CXX object
CMakeFiles/gmsh.dir/contrib/bamg/bamglib/MeshWrite.cpp.o
[100%] Building CXX object
CMakeFiles/gmsh.dir/contrib/bamg/bamglib/Meshio.cpp.o [100%] Building CXX
object
CMakeFiles/gmsh.dir/contrib/bamg/bamglib/QuadTree.cpp.o
make[2]: *** No rule to make target `/usr/lib64/libcblas.so', needed
by `gmsh'. Stop.
This looks strange. A target in the root file system? Here the log continues
like this:
[100%] Building CXX object
CMakeFiles/gmsh.dir/contrib/bamg/bamglib/Meshio.cpp.o
[100%] Building CXX object
CMakeFiles/gmsh.dir/contrib/bamg/bamglib/QuadTree.cpp.o
[100%] Building CXX object
CMakeFiles/gmsh.dir/contrib/bamg/bamglib/SetOfE4.cpp.o
Linking CXX executable gmsh
[100%] Built target gmsh
Source compiled.
Test phase [not enabled]: sci-libs/gmsh-2.5.0
Does anyone have an idea of how solve this problem?
No. All I can say is that I just emerged gmsh without problems on ~amd64,
both with and without the blas USE flag. The other USE flags are those:
Installed versions: 2.5.0{tbz2}(23:10:59 26.08.2011)(X blas jpeg png
zlib -cgns -chaco -doc -examples -lua -med -metis -mpi -netgen -opencascade
-petsc -taucs -tetgen)
Wonko
