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Problem with v2.8.6 installation: CBLAS/LAPack
10-20-2009, 10:54
Post: #1
Question Problem with v2.8.6 installation: CBLAS/LAPack
Dear Emmanuel and SExtractor users.

I am having trouble installing v2.8.6 from the source.
After properly configuring the fftw (see previous posts), I get an error regarding the CBLAS/lapack libraries:

configure: error: CBLAS/LAPack library files not found at usual locations! Exiting.

I have the ATLAS libraries installed, so should have CBLAS and lapack. I could not find other simple ways to install these libraries.

I am using mac OS X 10.5.8, but my students reported having the same problem with some linux flavors, while attempting to install v2.8.6. So I believe this could be a quite common issue that other users are facing.

No problems installing v2.5.0 though.

Thanks!

Martin.

P.S.: This is some of the output while running ./configure :

[...]
checking for fftw_init_threads in -lfftw3_threads... yes
checking cblas.h usability... yes
checking cblas.h presence... yes
checking for cblas.h... yes
checking clapack.h usability... no
checking clapack.h presence... no
checking for clapack.h... no
checking for clapack_dpotrf in -llapack... no
checking for cblas_dgemm in -lcblas... yes
checking for clapack_dpotrf in -llapack... no
checking for cblas_dgemm in -lcblas... yes
checking for clapack_dpotrf in -llapack... no
checking for cblas_dgemm in -lcblas... yes
checking for clapack_dpotrf in -llapack... no
checking for cblas_dgemm in -lcblas... yes
checking for clapack_dpotrf in -llapack... no
checking for cblas_dgemm in -lcblas... yes
configure: error: CBLAS/LAPack library files not found at usual locations! Exiting.
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11-03-2009, 22:47 (This post was last modified: 11-03-2009 22:48 by Emmanuel Bertin.)
Post: #2
RE: Problem with v2.8.6 installation: CBLAS/LAPack
Hi Martin,

SExtractor uses the ATLAS implementation of Lapack. Most probably your Lapack library is the regular FORTRAN one. You might want to check out this thread until a Mac addict helps me finding a way to simplify installation on OS X Big Grin!
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11-13-2009, 15:31
Post: #3
Rolleyes RE: Problem with v2.8.6 installation: CBLAS/LAPack
I have the same problem with my Xubuntu Jaunty as well: Sad

checking cblas.h usability... yes
checking cblas.h presence... yes
checking for cblas.h... yes
checking clapack.h usability... yes
checking clapack.h presence... yes
checking for clapack.h... yes
checking for clapack_dpotrf in -llapack... no
checking for cblas_dgemm in -lcblas... yes
checking for clapack_dpotrf in -llapack... no
checking for cblas_dgemm in -lcblas... yes
checking for clapack_dpotrf in -llapack... no
checking for cblas_dgemm in -lcblas... yes
checking for clapack_dpotrf in -llapack... yes
checking for cblas_dgemm in -lcblas... yes
checking for cblas_dgemm in -lptcblas... no
configure: error: CBLAS/LAPack was compiled without multithreading support! Exiting.

Is there a way to fix this?
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01-21-2010, 11:52
Post: #4
RE: Problem with v2.8.6 installation: CBLAS/LAPack
Hi Martin,

Quote:configure: error: CBLAS/LAPack was compiled without multithreading support! Exiting.
Is there a way to fix this?
To guarantee maximum compatibility with older generations of machines, the binary version of ATLAS that comes in Linux distributions is often compiled with very restrictive configure options (no support for multithreading or SIMD instructions). For optimum performance it is therefore strongly recommended to compile ATLAS (and FFTW) yourself. Otherwise you may have to disable multithreading support in SExtractor with the --disable-threads configure option. Note that the SVN version of SExtractor (and SCAMP) print a warning instead of exiting in error. A new release is in the works.
- Emmanuel.
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02-03-2010, 14:22
Post: #5
RE: Problem with v2.8.6 installation: CBLAS/LAPack
Did you find a solution? becasuse I am a new user in linux and I have the same problem with CBLAS/LAPack, could somebody help me?
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02-03-2010, 15:16
Post: #6
RE: Problem with v2.8.6 installation: CBLAS/LAPack - possible solution
Hi,

I had the same problem describe in previous posts, i.e. the message
configure: error: CBLAS/LAPack library files not found at usual locations! Exiting

This in a fedora 8 64-bit PC.

Inspecting the file config.log, I found that the actual cause of the problem were undefined symbols in liblapack.so:
/usr/pkg/SIEvarios/ATLAS/x86_64/ATLAS-3.8.2/lib/liblapack.so: undefined reference to `cgemv_' (and a long list of other undefined references).

In my ATLAS installation (3.8.2, compiled from source) such symbols are indeed undefined in liblapack.so, and are defined instead in libf77blas.so.

The fix that worked for me was to edit the configure script, and add -lf77blas to each line containing -latlas and/or -llapack, for instance
LIBS="-llapack -lcblas -latlas -lm $LIBS" became
LIBS="-llapack -lcblas -latlas -lf77blas -lm $LIBS"
and so on.

The same problem showed up when compiling scamp, and was solved with the same trick.

I don't know whether this fix applies to other ATLAS installations/configurations, but perhaps it's worth a try.

Cheers
Nicola
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02-08-2010, 00:07
Post: #7
RE: Problem with v2.8.6 installation: CBLAS/LAPack
Thanks Nicola for sharing the trick. Weird though; I run ATLAS 3.8.3 (latest stable) and I don't have this problem.
- Emmanuel.
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06-26-2017, 20:37
Post: #8
RE: Problem with v2.8.6 installation: CBLAS/LAPack
I encountered the same issue of CBLAS/LAPack not being found, on Fedora 25 for SExtractor-2.19.5 even though ATLAS and all development packages were installed. I found this solution on a Mac forum which requires editing the ./configure script (very similar to Nicola's solution):

sed -i './configure' -e 's/-llapack/-ltatlas/' -e 's/-lcblas/-ltatlas/' -e 's/-latlas/-ltatlas/' -e 's/-lptcblas/-ltatlas/'

after that ./configure ran and make did its thing.

Christopher
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09-25-2017, 13:47
Post: #9
RE: Problem with v2.8.6 installation: CBLAS/LAPack
configure Sextractor 2.19.5 failed
kubuntu 14.04 LTS (16.04 too)

.....
checking cblas.h usability... yes
checking cblas.h presence... yes
checking for cblas.h... yes
checking clapack.h usability... no
checking clapack.h presence... no
checking for clapack.h... no
checking for clapack_dpotrf in -ltatlas... no
checking for cblas_dgemm in -ltatlas... no
checking for clapack_dpotrf in -ltatlas... no
checking for cblas_dgemm in -ltatlas... no
checking for clapack_dpotrf in -ltatlas... no
checking for cblas_dgemm in -ltatlas... no
checking for clapack_dpotrf in -ltatlas... no
checking for cblas_dgemm in -ltatlas... no
checking for clapack_dpotrf in -ltatlas... no
checking for cblas_dgemm in -ltatlas... no
configure: error: CBLAS/LAPack library files not found at usual locations! Exiting.


/utils/sextractor-2.19.5$ dpkg -l|grep atlas
ii libatlas-base-dev 3.10.1-4 amd64 Automatically Tuned Linear Algebra Software, generic static
ii libatlas-dev 3.10.1-4 all Automatically Tuned Linear Algebra Software, C header files
ii libatlas-doc 3.10.1-4 all Automatically Tuned Linear Algebra Software, documentation
ii libatlas3-base 3.10.1-4 amd64 Automatically Tuned Linear Algebra Software, generic shared


/utils/sextractor-2.19.5$ dpkg -l|grep blas
ii libblas-dev 1.2.20110419-7 amd64 Basic Linear Algebra Subroutines 3, static library
ii libblas-doc 1.2.20110419-7 all Basic Linear Algebra Subroutines 3, documentation
ii libblas-test 1.2.20110419-7 amd64 Basic Linear Algebra Subroutines 3, testing programs
ii libblas3 1.2.20110419-7 amd64 Basic Linear Algebra Reference implementations, shared library
ii libblas3gf 1.2.20110419-7 all Transitional package for libblas
ii liblastfm1:amd64 1.0.8-2 amd64 Last.fm web services library
ii libopenblas-base 0.2.8-6ubuntu1 amd64 Optimized BLAS (linear algebra) library based on GotoBLAS2
ii libopenblas-dev 0.2.8-6ubuntu1 amd64 Optimized BLAS (linear algebra) library based on GotoBLAS2

I did above tricks - still same error. Please help me,
Thanks, Harald
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09-25-2017, 22:56
Post: #10
RE: Problem with v2.8.6 installation: CBLAS/LAPack
Hi Harald,
in any case, you can download and try my free open project Ubuntu Astronomy 16.04 (64-bit).
It has SExtractor version 2.23.2.

Ok.
SExtractor needs these libraries:
Code:
sudo apt-get install libatlas-dev libatlas3-base libatlas-base-dev

Open the directory with SExtractor source code and run:
Code:
./configure --with-atlas-libdir=/usr/lib/ --with-atlas-incdir=/usr/include/atlas
make
sudo make install

My OS is Astronomy Linux 19.04 (64-bit) https://astronomylinux.ap-i.net
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