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jody
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Posts: 460
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PostPosted: Mon Aug 19, 2013 4:56 pm    Post subject: Overlay problem: emerging package from overlay Reply with quote

Hi

I have an application which needs liblapack.a.
In earlier times i could 'emerge sci-libs/lapack-atlas' which would install the library.

Since some time there is no more 'sci-libs/lapack-atlas'.
In a different post somebody suggested to use the Overlay 'zugaina' and get atlas from there.
(http://gpo.zugaina.org/Overlays/science/sci-libs/atlas)
I have installed layman and added zugaina:
Code:
 ~ # layman -l

 * zugaina                   [Rsync     ] (rsync://gentoo.zugaina.org/zugaina-portage                              )


and my '/etc/portage/make.conf' contains the line
Code:
source /var/lib/layman/make.conf


But if i want to emerge 'sci-libs/atlas', this fails:
Code:
 ~ # emerge sci-libs/atlas
Calculating dependencies... done!

emerge: there are no ebuilds to satisfy "sci-libs/atlas".

emerge: searching for similar names...
emerge: Maybe you meant any of these: sci-libs/taucs, sci-libs/lis, sci-libs/gts?


Can somebody see what i am doing wrong here?

Thank You
Jody
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creaker
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PostPosted: Mon Aug 19, 2013 5:23 pm    Post subject: Reply with quote

sci-libs/atlas located in 'science' overlay, not in zugaina:

Code:
layman -a science
emerge -av sci-libs/atlas

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dol-sen
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PostPosted: Tue Aug 20, 2013 12:15 am    Post subject: Reply with quote

Yes, the website is a general overlay search engine. It lists the overlay it comes from in the lower right corner of the listing.

What creaker said ;)
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Porthole, the Portage GUI frontend irc@freenode: #gentoo-guis, #porthole, Blog
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Last edited by dol-sen on Tue Aug 20, 2013 9:38 pm; edited 1 time in total
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jody
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PostPosted: Tue Aug 20, 2013 11:07 am    Post subject: Reply with quote

Thank You for your replies.

I added the science overlay and was now able to start building sci-libs/atlas after (temporarily) unmerging eselect-cblas, eselect-blas, eselect-lapack which were blocking atlas,
but then it failed:
Code:
/usr/bin/gcc -o ATL_dtrsmLLTN.o -c -DL2SIZE=4194304 -I/var/tmp/portage/sci-libs/atlas-3.10.1-r1/work/ATLAS_shared/include -I/var/tmp/portage/sci-libs/atlas-3.10.1-r1/work/ATLAS//include -I/var/tmp/portage/sci-libs/atlas-3.10.1-r1/work/ATLAS//include/contrib -DAdd_ -DF77_INTEGER=int -DStringSunStyle -DATL_OS_Linux -DATL_ARCH_Corei2 -DATL_CPUMHZ=3601 -DATL_AVX -DATL_SSE3 -DATL_SSE2 -DATL_SSE1 -DATL_USE64BITS -DATL_GAS_x8664 -m64 -DWALL -DATL_NCPU=8 -O2 -pipe -ggdb -fPIC -m64 -DDREAL -DLower_ \
         -DTranspose_ -DNonUnitDiag_ /var/tmp/portage/sci-libs/atlas-3.10.1-r1/work/ATLAS//src/blas/level3/kernel/ATL_trsmL.c
/var/tmp/portage/sci-libs/atlas-3.10.1-r1/work/ATLAS//src/blas/level3/kernel/ATL_trsmKL_rk4.c: In function 'ATL_rk4':
/var/tmp/portage/sci-libs/atlas-3.10.1-r1/work/ATLAS//src/blas/level3/kernel/ATL_trsmKL_rk4.c:31:4: error: unknown type name '__m256d'
/var/tmp/portage/sci-libs/atlas-3.10.1-r1/work/ATLAS//src/blas/level3/kernel/ATL_trsmKL_rk4.c:32:4: error: unknown type name '__m256d'
/var/tmp/portage/sci-libs/atlas-3.10.1-r1/work/ATLAS//src/blas/level3/kernel/ATL_trsmKL_rk4.c:33:4: error: unknown type name '__m256d'
/var/tmp/portage/sci-libs/atlas-3.10.1-r1/work/ATLAS//src/blas/level3/kernel/ATL_trsmKL_rk4.c:34:4: error: unknown type name '__m256d'
/var/tmp/portage/sci-libs/atlas-3.10.1-r1/work/ATLAS//src/blas/level3/kernel/ATL_trsmKL_rk4.c:35:4: error: unknown type name '__m256d'
/var/tmp/portage/sci-libs/atlas-3.10.1-r1/work/ATLAS//src/blas/level3/kernel/ATL_trsmKL_rk4.c:53:7: error: unknown type name '__m256d'
/var/tmp/portage/sci-libs/atlas-3.10.1-r1/work/ATLAS//src/blas/level3/kernel/ATL_trsmKL_rk4.c:142:7: error: unknown type name '__m256d'
/var/tmp/portage/sci-libs/atlas-3.10.1-r1/work/ATLAS//src/blas/level3/kernel/ATL_trsmKL_rk4.c:186:7: error: unknown type name '__m256d'
make[5]: *** [ATL_dtrsmKL_rk4.o] Error 1
make[5]: *** Waiting for unfinished jobs....
/var/tmp/portage/sci-libs/atlas-3.10.1-r1/work/ATLAS//src/blas/level3/kernel/ATL_trsmKR_rk4.c: In function 'ATL_rk4':
/var/tmp/portage/sci-libs/atlas-3.10.1-r1/work/ATLAS//src/blas/level3/kernel/ATL_trsmKR_rk4.c:31:4: error: unknown type name '__m256d'
/var/tmp/portage/sci-libs/atlas-3.10.1-r1/work/ATLAS//src/blas/level3/kernel/ATL_trsmKR_rk4.c:32:4: error: unknown type name '__m256d'
/var/tmp/portage/sci-libs/atlas-3.10.1-r1/work/ATLAS//src/blas/level3/kernel/ATL_trsmKR_rk4.c:33:4: error: unknown type name '__m256d'
/var/tmp/portage/sci-libs/atlas-3.10.1-r1/work/ATLAS//src/blas/level3/kernel/ATL_trsmKR_rk4.c:34:4: error: unknown type name '__m256d'
/var/tmp/portage/sci-libs/atlas-3.10.1-r1/work/ATLAS//src/blas/level3/kernel/ATL_trsmKR_rk4.c:35:4: error: unknown type name '__m256d'
/var/tmp/portage/sci-libs/atlas-3.10.1-r1/work/ATLAS//src/blas/level3/kernel/ATL_trsmKR_rk4.c:53:7: error: unknown type name '__m256d'
/var/tmp/portage/sci-libs/atlas-3.10.1-r1/work/ATLAS//src/blas/level3/kernel/ATL_trsmKR_rk4.c:142:7: error: unknown type name '__m256d'
/var/tmp/portage/sci-libs/atlas-3.10.1-r1/work/ATLAS//src/blas/level3/kernel/ATL_trsmKR_rk4.c:186:7: error: unknown type name '__m256d'
make[5]: *** [ATL_dtrsmKR_rk4.o] Error 1
make[5]: Leaving directory `/var/tmp/portage/sci-libs/atlas-3.10.1-r1/work/ATLAS_shared/src/blas/level3/kernel'
make[4]: *** [dlib] Error 2
make[4]: Leaving directory `/var/tmp/portage/sci-libs/atlas-3.10.1-r1/work/ATLAS_shared/src/blas/level3/kernel'
make[3]: *** [dkern] Error 2
make[3]: Leaving directory `/var/tmp/portage/sci-libs/atlas-3.10.1-r1/work/ATLAS_shared/src/blas/level3'
make[2]: *** [IBuildLibs] Error 2
make[2]: Leaving directory `/var/tmp/portage/sci-libs/atlas-3.10.1-r1/work/ATLAS_shared/bin'
   DONE  STAGE 5-1-0 at 12:46




ATLAS install complete.  Examine
ATLAS/bin/<arch>/INSTALL_LOG/SUMMARY.LOG for details.
make[1]: Leaving directory `/var/tmp/portage/sci-libs/atlas-3.10.1-r1/work/ATLAS_shared'
make clean
make[1]: Entering directory `/var/tmp/portage/sci-libs/atlas-3.10.1-r1/work/ATLAS_shared'
rm -f *.o x* config?.out *core*
make[1]: Leaving directory `/var/tmp/portage/sci-libs/atlas-3.10.1-r1/work/ATLAS_shared'
make -j5 libclapack.a
make: *** No rule to make target `liblapack.a', needed by `libclapack.a'.  Stop.
 * ERROR: sci-libs/atlas-3.10.1-r1 failed (compile phase):
 *   emake failed
 *
 * If you need support, post the output of `emerge --info '=sci-libs/atlas-3.10.1-r1'`,
 * the complete build log and the output of `emerge -pqv '=sci-libs/atlas-3.10.1-r1'`.
 * This ebuild is from an overlay named 'science': '/var/lib/layman/science/'
 * The complete build log is located at '/var/tmp/portage/sci-libs/atlas-3.10.1-r1/temp/build.log'.
 * The ebuild environment file is located at '/var/tmp/portage/sci-libs/atlas-3.10.1-r1/temp/environment'.
 * Working directory: '/var/tmp/portage/sci-libs/atlas-3.10.1-r1/work/ATLAS_shared/lib'
 * S: '/var/tmp/portage/sci-libs/atlas-3.10.1-r1/work/ATLAS'

>>> Failed to emerge sci-libs/atlas-3.10.1-r1, Log file:

>>>  '/var/tmp/portage/sci-libs/atlas-3.10.1-r1/temp/build.log'

There seem to be two problems:
- the unknown type name '__m256d'
- the attempt to build liblapack.a in order to build libclapack.a.
This is especiallz strange since liblapack is present:
Code:
 # ls -l /usr/lib64/liblapack.*
lrwxrwxrwx 1 root root 28 Aug 20 09:43 /usr/lib64/liblapack.a -> lapack/reference/liblapack.a
lrwxrwxrwx 1 root root 29 Aug 20 09:43 /usr/lib64/liblapack.so -> lapack/reference/liblapack.so
lrwxrwxrwx 1 root root 31 Aug 20 09:43 /usr/lib64/liblapack.so.0 -> lapack/reference/liblapack.so.0

and
Code:
 # equery belongs /usr/lib64/liblapack.a
 * Searching for /usr/lib64/liblapack.a ...
sci-libs/lapack-reference-3.1.1-r1 (/usr/lib64/lapack/reference/liblapack.a)


At least once, further up in the buyilding of sci-atlas, there was:
Code:

ERROR IN COMMAND: make mmucaseN mmrout=SSEGENOUTDIR/dgenmm_sse.c moves="" casnam=res/dmmNMK10037_TN60x60x60_2x3x60_0_0x0x0_0_0_a1_b1_0 pre=d M=60 N=60 K=60 mb=60 nb=60 kb=60 mu=2 nu=3 ku=60 lda=60 ldb=60 ldc=0 beta=1 > /dev/null 2>&1
   PROPOSED FILENAME: res/dmmNMK10037_TN60x60x60_2x3x60_0_0x0x0_0_0_a1_b1_0
   GENSTR='make dgensseK mu=2 nu=3 ku=60 MB=60 NB=60, KB=60 dssegenf=SSEGENOUTDIR/dgenmm_sse.c lda=60 ldb=60 ldc=0 ssegenflags="-treatLoadsAsFloat 1 -treatStoresAsFloat 1 -prefetchABlock 1 -prefetchBCols 1" > /dev/null 2>&1
'
Default compiler & flags do not support SSEGEN!!

I don't know what SSEGEN is, but it seems not to be severe because the build continued...

Is there some package on which atlas depends which i have not installed?
Or have i mad some other mistake?
Thank You
Jody
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