Re: [easybuild] undefined reference to 'omp_get_num_threads' despite openmp=True

[Alan O'Cais]

Yeah, something like
preconfigopts = 'export LDFLAGS="-fopenmp $LDFLAGS" && '

On Mon, 23 Mar 2020 at 14:18, Ward Poelmans 
mailto:wpoel...@gmail.com>> wrote:
On 23/03/2020 14:08, Loris Bennett wrote:
> So the libraries seem to get build OK, but linking the client against
> them seems to fail, despite the fact that all the calls to 'gcc' seem to
> have the option '-fopenmp' set.

The issue is that the last one (--mode=link) does not have -fopenmp.
Either you need to add it to the link flags or manually add -lgomp to
the libraries to link to.

Ward


--
Dr. Alan O'Cais
E-CAM Software Manager
Juelich Supercomputing Centre
Forschungszentrum Juelich GmbH
52425 Juelich, Germany

Phone: +49 2461 61 5213
Fax: +49 2461 61 6656
E-mail: a.oc...@fz-juelich.de
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Prof. Dr. Sebastian M. Schmidt

Re: [easybuild] undefined reference to 'omp_get_num_threads' despite openmp=True

[Ward Poelmans]

On 23/03/2020 14:08, Loris Bennett wrote:
> So the libraries seem to get build OK, but linking the client against
> them seems to fail, despite the fact that all the calls to 'gcc' seem to
> have the option '-fopenmp' set.

The issue is that the last one (--mode=link) does not have -fopenmp.
Either you need to add it to the link flags or manually add -lgomp to
the libraries to link to.

Ward

Re: [easybuild] Locally modifying someone else's PR?

[Loris Bennett]

Dear Kenneth,

Kenneth Hoste  writes:

> Dear Loris,
>
> On 18/03/2020 10:42, Loris Bennett wrote:
>> Hi,
>>
>> If I have Github integration set up and I want to make changes to
>> someone else's PR, what would be the best workflow for that?
>
> This use case is not particularly well supported right now in EasyBuild 
> itself,
> since it involves pulling in the branch used for that PR first.
>
> Here's what I usually do:
>
> 1) Add the fork of the PR author using "git remote add AUTHOR URL", where 
> AUTHOR
> is the PR author's GitHub account, and URL is the URL to their fork (see "git
> remote -v" for inspiration).
>
> 2) Pull in their branches, using "git fetch AUTHOR".
>
> 3) Check out their branch, using "git checkout PR_BRANCH_NAME"
>
> 4) Make changes
>
> 5) Send a PR to their branch, using "eb --new-pr --pr-target-account ACCOUNT
> --pr-target-branch PR_BRANCH_NAME ...", where you replace the "..." with the
> changed easyconfigs.
>
> You can use "eb --new-pr -D" or "eb --new-pr -x" here first to double check on
> yourself.
>
>
> There's a couple of caveats to this, but it usually works out well.

Thanks, I'll try that out.

Cheers,

Loris

-- 
Dr. Loris Bennett (Mr.)
ZEDAT, Freie Universität Berlin Email loris.benn...@fu-berlin.de

Re: [easybuild] undefined reference to 'omp_get_num_threads' despite openmp=True

[Loris Bennett]

Hi Ward,

Ward Poelmans  writes:

> Hi Loris,
>
> On 23/03/2020 13:25, Loris Bennett wrote:
>> 
>> ../lib/.libs/libgretl-1.0.so: error: undefined reference to 
>> 'omp_get_num_threads'
>> ../lib/.libs/libgretl-1.0.so: error: undefined reference to 'GOMP_barrier'
>> ../lib/.libs/libgretl-1.0.so: error: undefined reference to 
>> 'omp_get_thread_num'
>> ../lib/.libs/libgretl-1.0.so: error: undefined reference to 'GOMP_parallel'
>> ../lib/.libs/libgretl-1.0.so: error: undefined reference to 'omp_get_wtime'
>> ../lib/.libs/libgretl-1.0.so: error: undefined reference to 
>> 'omp_set_num_threads'
>> collect2: error: ld returned 1 exit status
>
> This means the linker is not pulling in `-lgomp`. I guess because
> `-fopenmp` is not used? The lines you show here above the errors are
> probably unrelated (can happen if you're not using -j1).

Thanks for the hint.  Here's the part of the log with --parallel=1:

libtool: link: (cd ".libs" && rm -f "libgretl-1.0.so.32" && ln -s 
"libgretl-1.0.so.32.0.0" "libgretl-1.0.so.32")
libtool: link: (cd ".libs" && rm -f "libgretl-1.0.so" && ln -s 
"libgretl-1.0.so.32.0.0" "libgretl-1.0.so")
libtool: link: ( cd ".libs" && rm -f "libgretl-1.0.la" && ln -s 
"../libgretl-1.0.la" "libgretl-1.0.la" )
make[1]: Leaving directory 
`/trinity/shared/easybuild/build/gretl/2020a/foss-2019a/gretl-2020a/lib'
make -C cli
make[1]: Entering directory 
`/trinity/shared/easybuild/build/gretl/2020a/foss-2019a/gretl-2020a/cli'
mkdir .deps
gcc -c -O2 -ftree-vectorize -march=native -fno-math-errno -fopenmp -I.. -I.. 
-I../lib/src  
-I/trinity/shared/easybuild/software/GLib/2.60.1-GCCcore-8.2.0/include/glib-2.0 
-I/trinity/shared/easybuild/software/GLib/2.60.1-GCCcore-8.2.0/lib/glib-2.0/include
 -I/trinity/shared/easybuild/software/PCRE/8.43-GCCcore-8.2.0/include   
-DLOCALEDIR=\"/trinity/shared/easybuild/software/gretl/2020a-foss-2019a/share/locale\"
 -DHAVE_CONFIG_H gretlcli.c
gcc -O2 -ftree-vectorize -march=native -fno-math-errno -fopenmp -I.. -I.. 
-I../lib/src  
-I/trinity/shared/easybuild/software/GLib/2.60.1-GCCcore-8.2.0/include/glib-2.0 
-I/trinity/shared/easybuild/software/GLib/2.60.1-GCCcore-8.2.0/lib/glib-2.0/include
 -I/trinity/shared/easybuild/software/PCRE/8.43-GCCcore-8.2.0/include   
-DLOCALEDIR=\"/trinity/shared/easybuild/software/gretl/2020a-foss-2019a/share/locale\"
 -DHAVE_CONFIG_H -MM gretlcli.c > .deps/gretlcli.d
gcc -c -O2 -ftree-vectorize -march=native -fno-math-errno -fopenmp -I.. -I.. 
-I../lib/src  
-I/trinity/shared/easybuild/software/GLib/2.60.1-GCCcore-8.2.0/include/glib-2.0 
-I/trinity/shared/easybuild/software/GLib/2.60.1-GCCcore-8.2.0/lib/glib-2.0/include
 -I/trinity/shared/easybuild/software/PCRE/8.43-GCCcore-8.2.0/include   
-DLOCALEDIR=\"/trinity/shared/easybuild/software/gretl/2020a-foss-2019a/share/locale\"
 -DHAVE_CONFIG_H complete.c
gcc -O2 -ftree-vectorize -march=native -fno-math-errno -fopenmp -I.. -I.. 
-I../lib/src  
-I/trinity/shared/easybuild/software/GLib/2.60.1-GCCcore-8.2.0/include/glib-2.0 
-I/trinity/shared/easybuild/software/GLib/2.60.1-GCCcore-8.2.0/lib/glib-2.0/include
 -I/trinity/shared/easybuild/software/PCRE/8.43-GCCcore-8.2.0/include   
-DLOCALEDIR=\"/trinity/shared/easybuild/software/gretl/2020a-foss-2019a/share/locale\"
 -DHAVE_CONFIG_H -MM complete.c > .deps/complete.d
../libtool --mode=link gcc -mavx -Winline  
-L/trinity/shared/easybuild/software/MPFR/4.0.2-GCCcore-8.2.0/lib 
-L/trinity/shared/easybuild/software/ImageMagick/7.0.8-46-GCCcore-8.2.0/lib 
-L/trinity/shared/easybuild/software/GtkSourceView/3.24.11-GCCcore-8.2.0/lib 
-L/trinity/shared/easybuild/software/GMP/6.1.2-GCCcore-8.2.0/lib 
-L/trinity/shared/easybuild/software/libxml2/2.9.8-GCCcore-8.2.0/lib 
-L/trinity/shared/easybuild/software/FFTW/3.3.8-gompi-2019a/lib 
-L/trinity/shared/easybuild/software/ScaLAPACK/2.0.2-gompi-2019a-OpenBLAS-0.3.5/lib
 -L/trinity/shared/easybuild/software/OpenBLAS/0.3.5-GCC-8.2.0-2.31.1/lib 
-L/trinity/shared/easybuild/software/GCCcore/8.2.0/lib64 
-L/trinity/shared/easybuild/software/GCCcore/8.2.0/lib -o gretlcli gretlcli.o 
complete.o \
../lib/libgretl-1.0.la -lreadline -lncurses
libtool: link: gcc -mavx -Winline -o .libs/gretlcli gretlcli.o complete.o  
-L/trinity/shared/easybuild/software/MPFR/4.0.2-GCCcore-8.2.0/lib 
-L/trinity/shared/easybuild/software/ImageMagick/7.0.8-46-GCCcore-8.2.0/lib 
-L/trinity/shared/easybuild/software/GtkSourceView/3.24.11-GCCcore-8.2.0/lib 
-L/trinity/shared/easybuild/software/GMP/6.1.2-GCCcore-8.2.0/lib 
-L/trinity/shared/easybuild/software/libxml2/2.9.8-GCCcore-8.2.0/lib 
-L/trinity/shared/easybuild/software/FFTW/3.3.8-gompi-2019a/lib 
-L/trinity/shared/easybuild/software/ScaLAPACK/2.0.2-gompi-2019a-OpenBLAS-0.3.5/lib
 -L/trinity/shared/easybuild/software/OpenBLAS/0.3.5-GCC-8.2.0-2.31.1/lib 
-L/trinity/shared/easybuild/software/GCCcore/8.2.0/lib64 
-L/trinity/shared/easybuild/software/GCCcore/8.2.0/lib 
../lib/.libs/libgretl-1.0.so 
-L/trinity/shared/easybuild/software/XZ/5.2.4-GCCcore-8.2.0/lib 
-L/trinity/shared/e

Re: [easybuild] Locally modifying someone else's PR?

[Kenneth Hoste]

Dear Loris,

On 18/03/2020 10:42, Loris Bennett wrote:

Hi,

If I have Github integration set up and I want to make changes to
someone else's PR, what would be the best workflow for that?


This use case is not particularly well supported right now in EasyBuild 
itself, since it involves pulling in the branch used for that PR first.


Here's what I usually do:

1) Add the fork of the PR author using "git remote add AUTHOR URL", 
where AUTHOR is the PR author's GitHub account, and URL is the URL to 
their fork (see "git remote -v" for inspiration).


2) Pull in their branches, using "git fetch AUTHOR".

3) Check out their branch, using "git checkout PR_BRANCH_NAME"

4) Make changes

5) Send a PR to their branch, using "eb --new-pr --pr-target-account 
ACCOUNT --pr-target-branch PR_BRANCH_NAME ...", where you replace the 
"..." with the changed easyconfigs.


You can use "eb --new-pr -D" or "eb --new-pr -x" here first to double 
check on yourself.



There's a couple of caveats to this, but it usually works out well.

regards,

Kenneth



Cheers,

Loris

Re: [easybuild] undefined reference to 'omp_get_num_threads' despite openmp=True

[Ward Poelmans]

Hi Loris,

On 23/03/2020 13:25, Loris Bennett wrote:
> 
> ../lib/.libs/libgretl-1.0.so: error: undefined reference to 
> 'omp_get_num_threads'
> ../lib/.libs/libgretl-1.0.so: error: undefined reference to 'GOMP_barrier'
> ../lib/.libs/libgretl-1.0.so: error: undefined reference to 
> 'omp_get_thread_num'
> ../lib/.libs/libgretl-1.0.so: error: undefined reference to 'GOMP_parallel'
> ../lib/.libs/libgretl-1.0.so: error: undefined reference to 'omp_get_wtime'
> ../lib/.libs/libgretl-1.0.so: error: undefined reference to 
> 'omp_set_num_threads'
> collect2: error: ld returned 1 exit status

This means the linker is not pulling in `-lgomp`. I guess because
`-fopenmp` is not used? The lines you show here above the errors are
probably unrelated (can happen if you're not using -j1).

Ward

[easybuild] undefined reference to 'omp_get_num_threads' despite openmp=True

[Loris Bennett]

Hi,

I'm trying to write an easyconfig for gretl[1].  I have

  toolchain = {'name': 'foss', 'version': '2019a'}
  toolchainopts = {'openmp': True}

but I am getting the following error:

libtool: compile:  gcc -mavx -Winline -c -O2 -ftree-vectorize -march=native 
-fno-math-errno -fopenmp -I.. -I../gui -DHAVE_CONFIG_H -I../lib/src -pthread 
-I/trinity/shared/easybuild/software/
GTK+/3.24.8-GCCcore-8.2.0/include/gtk-3.0 
-I/trinity/shared/easybuild/software/libepoxy/1.5.3-GCCcore-8.2.0/include 
-I/trinity/shared/easybuild/software/Gdk-Pixbuf/2.38.1-GCCcore-8.2.0/inclu
de/gdk-pixbuf-2.0 
-I/trinity/shared/easybuild/software/at-spi2-atk/2.32.0-GCCcore-8.2.0/include/at-spi2-atk/2.0
 -I/trinity/shared/easybuild/software/at-spi2-core/2.32.0-GCCcore-8.2.0/include
/at-spi-2.0 
-I/trinity/shared/easybuild/software/ATK/2.32.0-GCCcore-8.2.0/include/atk-1.0 
-I/trinity/shared/easybuild/software/Mesa/19.0.1-GCCcore-8.2.0/include 
-I/trinity/shared/easybuild/s
oftware/libdrm/2.4.97-GCCcore-8.2.0/include 
-I/trinity/shared/easybuild/software/libdrm/2.4.97-GCCcore-8.2.0/include/libdrm 
-I/trinity/shared/easybuild/software/DBus/1.13.8-GCCcore-8.2.0/inc
lude/dbus-1.0 
-I/trinity/shared/easybuild/software/DBus/1.13.8-GCCcore-8.2.0/lib/dbus-1.0/include
 
-I/trinity/shared/easybuild/software/Pango/1.43.0-GCCcore-8.2.0/include/pango-1.0
 -I/trinity
/shared/easybuild/software/FriBidi/1.0.5-GCCcore-8.2.0/include/fribidi 
-I/trinity/shared/easybuild/software/HarfBuzz/2.4.0-GCCcore-8.2.0/include/harfbuzz
 -I/trinity/shared/easybuild/software
/cairo/1.16.0-GCCcore-8.2.0/include/cairo 
-I/trinity/shared/easybuild/software/X11/20190311-GCCcore-8.2.0/include 
-I/trinity/shared/easybuild/software/fontconfig/2.13.1-GCCcore-8.2.0/include
 
-I/trinity/shared/easybuild/software/GLib/2.60.1-GCCcore-8.2.0/include/gio-unix-2.0
 -I/trinity/shared/easybuild/software/GLib/2.60.1-GCCcore-8.2.0/include 
-I/trinity/shared/easybuild/softwa
re/GLib/2.60.1-GCCcore-8.2.0/include/glib-2.0 
-I/trinity/shared/easybuild/software/GLib/2.60.1-GCCcore-8.2.0/lib/glib-2.0/include
 -I/trinity/shared/easybuild/software/util-linux/2.33-GCCcore
-8.2.0/include/uuid 
-I/trinity/shared/easybuild/software/util-linux/2.33-GCCcore-8.2.0/include/libmount
 
-I/trinity/shared/easybuild/software/util-linux/2.33-GCCcore-8.2.0/include/blkid
 -I/tr
inity/shared/easybuild/software/PCRE/8.43-GCCcore-8.2.0/include 
-I/trinity/shared/easybuild/software/libffi/3.2.1-GCCcore-8.2.0/include 
-I/trinity/shared/easybuild/software/expat/2.2.6-GCCco
re-8.2.0/include 
-I/trinity/shared/easybuild/software/pixman/0.38.0-GCCcore-8.2.0/include/pixman-1
 
-I/trinity/shared/easybuild/software/freetype/2.9.1-GCCcore-8.2.0/include/freetype2
 -I/trin
ity/shared/easybuild/software/libpng/1.6.36-GCCcore-8.2.0/include/libpng16 
-I/trinity/shared/easybuild/software/bzip2/1.0.6-GCCcore-8.2.0/include 
-I/trinity/shared/easybuild/software/zlib/1.
2.11-GCCcore-8.2.0/include 
-I/trinity/shared/easybuild/software/libxml2/2.9.8-GCCcore-8.2.0/include/libxml2
 -I../plugin 
-I/trinity/shared/easybuild/software/GLib/2.60.1-GCCcore-8.2.0/include
/glib-2.0 
-I/trinity/shared/easybuild/software/GLib/2.60.1-GCCcore-8.2.0/lib/glib-2.0/include
 -I/trinity/shared/easybuild/software/PCRE/8.43-GCCcore-8.2.0/include 
-I../plugin/zipunzip -I/tri
nity/shared/easybuild/software/GLib/2.60.1-GCCcore-8.2.0/include/glib-2.0 
-I/trinity/shared/easybuild/software/GLib/2.60.1-GCCcore-8.2.0/lib/glib-2.0/include
 -I/trinity/shared/easybuild/soft
ware/PCRE/8.43-GCCcore-8.2.0/include -I../plugin/libsvm 
-Wno-deprecated-declarations -I. vif.c  -fPIC -DPIC -o .libs/vif.o
../lib/.libs/libgretl-1.0.so: error: undefined reference to 
'omp_get_num_threads'
../lib/.libs/libgretl-1.0.so: error: undefined reference to 'GOMP_barrier'
../lib/.libs/libgretl-1.0.so: error: undefined reference to 'omp_get_thread_num'
../lib/.libs/libgretl-1.0.so: error: undefined reference to 'GOMP_parallel'
../lib/.libs/libgretl-1.0.so: error: undefined reference to 'omp_get_wtime'
../lib/.libs/libgretl-1.0.so: error: undefined reference to 
'omp_set_num_threads'
collect2: error: ld returned 1 exit status

Any ideas what I'm doing wrong?

Cheers,

Loris

Footnotes: 
[1]  http://gretl.sourceforge.net/

-- 
Dr. Loris Bennett (Mr.)
ZEDAT, Freie Universität Berlin Email loris.benn...@fu-berlin.de