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I am having trouble installing psfex  3.17.3+0 (part of the astromatic spring2015+0 meta-package) on an Ubuntu 14.04 system.

I ran the following eups commands:

eups distrib install pythonCore spring2015+0 --nolocks
eups distrib install pythonDESDM spring2015+0 --nolocks
eups distrib install astromatic spring2015+0 --nolocks
 
The first two worked, but the third failed at the psfex install step.
Here are the error messages:
---------------------------------------------------------------------------------------------
Installing psfex 3.17.3+0 for generic...
BUILD ERROR!  From build log:
checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE
checking if more special flags are required for pthreads... no
checking for cc_r... /usr/bin/gcc
checking /home/dtucker/Software/EUPS_DESDM/eups/packages/Linux64/fftw/3.3.2+5/include/fftw3.h usability... yes
checking /home/dtucker/Software/EUPS_DESDM/eups/packages/Linux64/fftw/3.3.2+5/include/fftw3.h presence... yes
checking for /home/dtucker/Software/EUPS_DESDM/eups/packages/Linux64/fftw/3.3.2+5/include/fftw3.h... yes
checking for fftwf_execute in -lfftw3f... yes
checking for fftwf_init_threads in -lfftw3f... no
checking for fftwf_init_threads in -lfftw3f_threads... yes
checking /home/dtucker/Software/EUPS_DESDM/eups/packages/Linux64/atlas_netlib/3.8.4+9/include/cblas.h usability... yes
checking /home/dtucker/Software/EUPS_DESDM/eups/packages/Linux64/atlas_netlib/3.8.4+9/include/cblas.h presence... yes
checking for /home/dtucker/Software/EUPS_DESDM/eups/packages/Linux64/atlas_netlib/3.8.4+9/include/cblas.h... yes
checking /home/dtucker/Software/EUPS_DESDM/eups/packages/Linux64/atlas_netlib/3.8.4+9/include/clapack.h usability... yes
checking /home/dtucker/Software/EUPS_DESDM/eups/packages/Linux64/atlas_netlib/3.8.4+9/include/clapack.h presence... yes
checking for /home/dtucker/Software/EUPS_DESDM/eups/packages/Linux64/atlas_netlib/3.8.4+9/include/clapack.h... yes
checking for clapack_dpotrf in -llapack_atlas... no
checking for cblas_dgemm in -lcblas... yes
checking for clapack_dpotrf in -llapack_atlas... (cached) no
checking for cblas_dgemm in -lcblas... no
configure: error: CBLAS/LAPack library files not found in /home/dtucker/Software/EUPS_DESDM/eups/packages/Linux64/atlas_netlib/3.8.4+9
eups distrib: Failed to build psfex-3.17.3+0.build: Command:
        export EUPS_PATH=/home/dtucker/Software/EUPS_DESDM/eups/packages
        (cd /home/dtucker/Software/EUPS_DESDM/eups/packages/EupsBuildDir/Linux64/psfex-3.17.3+0 &&
        setup --just --type=build swarp 2.38.0.1+0 &&
        setup --just --type=build sqlite 3080002+0 &&
        setup --just --type=build netlibLAPACK 3.4.1+2 &&
        setup --just --type=build libjpeg 8d+0 &&
        setup --just --type=build gettext 0.18.2+1 &&
        setup --just --type=build cdsclient 3.71+0 &&
        setup --just --type=build atlas_netlib 3.8.4+9 &&
        setup --just --type=build python 2.7.6+2 &&
        setup --just --type=build numpy 1.9.1+2 &&
        setup --just --type=build fftw 3.3.2+5 &&
        setup --just --type=build sextractor 2.20.2+0 &&
        set -o errexit
        set -o nounset
        shopt -s extglob
        EXTERNAL=http://desbuild.cosmology.illinois.edu/eeups/webservice/resources
                --enable-single --enable-threads
        fi
        make
        make install
        mkdir -p $PRODUCT_DIR/lib
        cp -a src/* $PRODUCT_DIR/lib) >> /home/dtucker/Software/EUPS_DESDM/eups/packages/EupsBuildDir/Linux64/psfex-3.17.3+0/psfex-3.1
exited with code 1
---------------------------------------------------------------------------------------------
But, the CBLAS/LAPack library files do appear to exist in /home/dtucker/Software/EUPS_DESDM/eups/packages/Linux64/atlas_netlib/3.8.4+9:

dtucker@Urania5:~$ ls -l /home/dtucker/Software/EUPS_DESDM/eups/packages/Linux64/atlas_netlib/3.8.4+9/lib/

total 19448

-rw-r--r-- 1 dtucker dtucker 8348668 Jun  8 15:51 libatlas.a

-rw-r--r-- 1 dtucker dtucker  467720 Jun  8 15:51 libcblas.a

-rw-r--r-- 1 dtucker dtucker  564386 Jun  8 15:51 libf77blas.a

-rw-r--r-- 1 dtucker dtucker 9489158 Jun  8 15:51 liblapack.a

-rw-r--r-- 1 dtucker dtucker  468278 Jun  8 15:51 libptcblas.a

-rw-r--r-- 1 dtucker dtucker  564946 Jun  8 15:51 libptf77blas.a

 

Any suggestions?

 

Thanks!

 

Best regards,

Douglas

 

PS:  (added 11 June 2015)  Here is the attached build file:  psfex-3.17.3+0.build.log .

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    5 answers

    1.  
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      Examining the 'config.log' in the psfex source directory shows us what is happening at one level:

      ...
      configure:14987: result: no
      configure:15000: checking for cblas_dgemm in -lcblas
      configure:15025: /usr/bin/gcc -o conftest -g -O2   conftest.c -lcblas -L/usr/local/lsst/eups/packages/Linux64/atlas_netlib/3.8.4+9/lib -latlas -lm  >&5
      configure:15025: $? = 0
      configure:15034: result: yes
      configure:15055: checking for clapack_dpotrf in -llapack_atlas
      configure:15090: result: no
      configure:15103: checking for cblas_dgemm in -lcblas
      configure:15128: /usr/bin/gcc -o conftest -g -O2   conftest.c -lcblas -L/usr/local/lsst/eups/packages/Linux64/atlas_netlib/3.8.4+9/lib/lib -latlas -lm -lcblas  >&5
      /usr/bin/ld: cannot find -lcblas
      /usr/bin/ld: cannot find -latlas
      /usr/bin/ld: cannot find -lcblas
      collect2: error: ld returned 1 exit status

       We can see an odd append of lib, i.e.,  .. atlas_netlib/3.8.4+9/lib/lib on the link line that fails. 

      So next step can be to try to determine why this occurring on ubuntu, how it might be fixed or patched, continuing investigation ...

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        I found this link of someone having trouble with sextractor/psfex + atlas + ubuntu, but I did not  learn anything from this yet :

        http://ubuntuforums.org/showthread.php?t=1325671

          CommentAdd your comment...
        1.  
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          I  have reproduced the problem on ubuntu 14.04 , so I have a work space to investigate (!!) 

          1. Douglas Tucker

            Thanks, Greg! I know you are busy and I appreciate the help!

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        2.  
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          Hi Douglas,  

              Can you see if the error repeats in a scenario where one first explicitly says

          % setup atlas_netlib 3.8.4+9 

          and then 

          eups distrib install psfex 3.17.3+0

          We observed behavior like this within a larger build where it looks like dependent packages do not always get setup. Not sure yet whether this is eups or python issue; I do not think I have ever seen it in years of building production stacks but we saw this the other day  on NERSC Edison (that case 'setuptools' not  being setup in the build of higher python modules).   I will see if I can reproduce the scenario on ubuntu 14.04. 



          1. Douglas Tucker

            Explicitly setting up atlas_netlib 3.8.4 did not seem to work: eups distrib install atlas_netlib 3.8.4+9 --force --nolocks setup atlas_netlib 3.8.4+9 eups distrib install psfex 3.17.3+0 resulted in the same error: ------------------------------ ... checking for clapack_dpotrf in -llapack_atlas... no checking for cblas_dgemm in -lcblas... yes checking for clapack_dpotrf in -llapack_atlas... (cached) no checking for cblas_dgemm in -lcblas... no configure: error: CBLAS/LAPack library files not found in /home/dtucker/Software/EUPS_DESDM/eups/packages/Linux64/atlas_netlib/3.8.4+9/lib! Exiting. eups distrib: Failed to build psfex-3.17.3+0.build: Command: ... ------------------------------

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          Douglas, could you email me or post the log file generated?

          1. Douglas Tucker

            Thanks, Felipe! I've attached the build log in the "PS:" at the end of my original question.

          2. Felipe Menanteau

            Can you try re-installing atlas_netlib 3.8.4+9? {code} eups distrib install atlas_netlib 3.8.4+9 --nolocks eups distrib install psfex 3.17.3+0 {code} You can also try psfex 3.17.3+1, {code} eups distrib install psfex 3.17.3+1 {code}

          3. Douglas Tucker

            Re-installing atlas_netlib 3.8.4+9 and then psfex 3.17.3+0 did not seem to work: eups distrib install atlas_netlib 3.8.4+9 --force --nolocks setup atlas_netlib 3.8.4+9 eups distrib install psfex 3.17.3+0 resulted in the same error: ------------------------------ ... checking for clapack_dpotrf in -llapack_atlas... no checking for cblas_dgemm in -lcblas... yes checking for clapack_dpotrf in -llapack_atlas... (cached) no checking for cblas_dgemm in -lcblas... no configure: error: CBLAS/LAPack library files not found in /home/dtucker/Software/EUPS_DESDM/eups/packages/Linux64/atlas_netlib/3.8.4+9/lib! Exiting. eups distrib: Failed to build psfex-3.17.3+0.build: Command: ... ------------------------------

          4. Douglas Tucker

            I also tried installing psfex 3.17.3+1, and I get the same error.

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