Re: OpenBLAS build failure on Catalina, was Re: Failures in installing pymol-py36 on Catalina

Dear Alexander,
your suggestion worked and made fink capable to install openblas and then pymol-py36.
Thank you again for your help and patience.
Cheers,
marco

Marco Patrone – PhD
Biocrystallography Unit
Division of Immunology, Transplantation, and Infectious Disease (DITID)
DIBIT – San Raffaele Scientific Institute
Via Olgettina, 58
20132 Milano
Italy
phone: +39 0226434921
fax: +39 0226434153
http://www.hsr.it/research/organzation/massimo-degano

________________________________
Da: Alexander Hansen <[email protected]>
Inviato: Mercoledì 27 Maggio 2020, 22:09
A: Patrone Marco
Cc: [email protected]; [email protected]
Oggetto: OpenBLAS build failure on Catalina, was Re: [Fink-beginners] Failures in installing pymol-py36 on Catalina



> On May 27, 2020, at 00:31, Patrone Marco <[email protected]> wrote:
>
> Dear All,
> I've just moved to MacOS Catalina on a new Mac laptop. I'm encountering several problems trying to install pymol-py36. I'm poorly skilled in Linux and Unix, so I'm just asking for explanations and, hopefully, for solutions.
> A first failure on installing term-readkey-pm5184-2.37-1 was solved following the suggestion found here:

<snip>  It is best to keep the focus of support requests on the package that is actually failing.

> other packages could be installed then, but I' stuck on openblas. Here is the error message
>
> marcopatrone@MBP-di-Marco ~ % sudo fink install pymol-py36

You normally shouldn’t need to use “sudo” before the “fink” command, and in rare instances that can even produce build failures.

<snip>

> #!/bin/sh -ev
> # set arch to minimum model supported in OS version
> darwin_vers=$(uname -r | cut -d. -f1)
> uname -r | cut -d. -f1
> if [ "$darwin_vers" -ge 18 ]; then
> perl -pi -e "s|(COMMON_OPT = -O2)|\$1 -mtune=cascadelake -march=ivybridge|g;" Makefile.system
> else
> perl -pi -e "s|(COMMON_OPT = -O2)|\$1 -mtune=cascadelake -march=core2|g;" Makefile.system
> fi
> make FC=gfortran-fsf-9 USE_THREAD=1 libs netlib shared
> Warning: Failed to set locale category LC_NUMERIC to en_IT.
> Warning: Failed to set locale category LC_TIME to en_IT.
> Warning: Failed to set locale category LC_COLLATE to en_IT.
> Warning: Failed to set locale category LC_MONETARY to en_IT.
> Warning: Failed to set locale category LC_MESSAGES to en_IT.
> Warning: Failed to set locale category LC_NUMERIC to en_IT.
> Warning: Failed to set locale category LC_TIME to en_IT.
> Warning: Failed to set locale category LC_COLLATE to en_IT.
> Warning: Failed to set locale category LC_MONETARY to en_IT.
> Warning: Failed to set locale category LC_MESSAGES to en_IT.
> Warning: Failed to set locale category LC_NUMERIC to en_IT.
> Warning: Failed to set locale category LC_TIME to en_IT.
> Warning: Failed to set locale category LC_COLLATE to en_IT.
> Warning: Failed to set locale category LC_MONETARY to en_IT.
> Warning: Failed to set locale category LC_MESSAGES to en_IT.
> Makefile:141: *** OpenBLAS: Detecting CPU failed. Please set TARGET explicitly, e.g. make TARGET=your_cpu_target. Please read README for the detail..  Stop.
> ### execution of /tmp/fink.SPSMh failed, exit code 2
> ### execution of /tmp/fink.ay9V6 failed, exit code 2
> Removing runtime build-lock...
> Removing build-lock package...
> /opt/sw/bin/dpkg-lockwait -r fink-buildlock-openblas-0.3.8-1
> (Reading database ... 32552 files and directories currently installed.)
> Removing fink-buildlock-openblas-0.3.8-1 ...
> Failed: phase compiling: openblas-0.3.8-1 failed
>
> Before reporting any errors, please run "fink selfupdate" and try again.
>
> If you continue to have issues, please check to see if the FAQ on Fink's
> website solves the problem.  If not, ask on one (not both, please) of
> these mailing lists:
>
> The Fink Users List <[email protected]>
> The Fink Beginners List <[email protected]>,
>
> with a carbon copy to the maintainer:
>
> Derek Homeier <[email protected]>
>
> Note that this is preferable to emailing just the maintainer directly,
> since most fink package maintainers do not have access to all possible
> hardware and software configurations.
>
> Please try to include the complete error message in your report.  This
> generally consists of a compiler line starting with e.g. "gcc" or "g++"
> followed by the actual error output from the compiler.
>
> Also include the following system information:
> Package manager version: 0.45.1
> Distribution version: selfupdate-rsync Mon May 25 21:51:19 2020, 10.15, x86_64
> Trees: local/main stable/main
> Xcode.app: 11.5
> Xcode command-line tools: 11.5.0.0.1.1588476445
> Max. Fink build jobs:  1
>
> I've tried the following:
>
> make clean
> make TARGET=NEHALEM
>
> as suggested in https://github.com/xianyi/OpenBLAS/issues/2227
>
> and then "make install"
> Apparently openblas was installed, not in /opt/sw but rather in a /opt/OpenBlas directory. Fink does not recognize its presence and tries to install it again when I run " fink install pymol-py36", ending up with the same failure.
>

You did a manual install.  By design, Fink tries to ignore those.

> I've changed the installation location in the Makefile.installation for openblas so to install it in /opt/sw  getting the following output
>
> marcopatrone@MBP-di-Marco OpenBLAS-0.3.8 % sudo make install
> /Applications/Xcode.app/Contents/Developer/usr/bin/make -j 8 -f Makefile.install install
> Generating openblas_config.h in /opt/sw/include
> Generating f77blas.h in /opt/sw/include
> Generating cblas.h in /opt/sw/include
> Copying the static library to /opt/sw/lib
> Copying the shared library to /opt/sw/lib
> Generating openblas.pc in /opt/sw/lib/pkgconfig
> Generating OpenBLASConfig.cmake in /opt/sw/lib/cmake/openblas
> Generating OpenBLASConfigVersion.cmake in /opt/sw/lib/cmake/openblas
> Install OK!
>
>
> but still fink doesn't sense its presence and makes again a failing installation of openblas.
>

Yes, because the database of installed packages doesn’t look for a package’s files to determine whether it is installed or not.

> What could I do?
>

The 'make TARGET=NEHALEM’ fix needs to be applied within the Fink package description (.info) file.  As noted earlier:
1)  Fink builds from clean sources, so any changes you make in the source tree are erased.
2)  Fink doesn’t recognize packages that it didn’t install (apart from a few exceptions), even if they are installed within its tree.

> Many thanks for your time.
> Best,
> marco
> --
> Marco Patrone - PhD
> Biocrystallography Unit
> Division of Immunology, Transplantation, and Infectious Diseases
> DIBIT - Scientific Institute San Raffaele
> Via Olgettina 58
> 20132 Milan
> Italy
> phone: +39-0226434921
> fax: +39-0226434153
> URL: http://www.sanraffaele.org/research/degano
>
>
> Rispetta l’ambiente: non stampare questa mail se non è necessario.
> Respect the environment: print this email only if necessary.
>


You could try editing /opt/sw/fink/dists/stable/main/finkinfo/sci/openblas.info and adding TARGET=NEHALEM on both of the “make” lines in the CompileScript block.  I’m not actually sure whether both of those need it, or just one.
--
Alexander Hansen, Ph.D.
Fink User Liaison

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