# Infinite configure run after executing make

**URL:** <https://discourse.abinit.org/t/infinite-configure-run-after-executing-make/3029>\
**Category:** Building Abinit\
**Created:** [November 9, 2021, 2:15pm UTC](https://discourse.abinit.org/t/infinite-configure-run-after-executing-make/3029 "2021-11-09T14:15:07Z")\
**Posts on this page:** 20\
**Page:** 1

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**Author:** ![mroyo](https://discourse.abinit.org/letter_avatar_proxy/v4/letter/m/e95f7d/32.png) [@mroyo](https://discourse.abinit.org/u/mroyo)\
**Post date:** [November 9, 2021, 2:15pm UTC](https://discourse.abinit.org/t/infinite-configure-run-after-executing-make/3029/1 "2021-11-09T14:15:07Z")

</div>

Hello,

I’m having a recurrent problem when I try to build ABINIT (it appears regardless the different version I’m building, ranging from v8.8 to the last one in the trunk/develop branch) in our local cluster.

For instance, if I clone my develop branch (which used to compile correctly few months ago) and I execute:

./autogen.sh

./configure --with-config-file=/home/mroyo/.abinit/build/supermat\_gomkl-2020b.ac

make

The first two commands seem to go fine. However “make” never starts the compilation, it instead runs the configure again and, what is worse, it enters an infinite loop in which it repeats the configure run again and again. The same happens if I try to run a “make clean” or a “make distclean”.

The only suspicious log messages that I can see are these ones:

./config.status: line 2290: /config/scripts/make-optim-dumper: No such file or directory

config.status: executing script-perms commands

config.status: executing source-split commands

config.status: executing long-lines commands

/bin/sh: /config/scripts/shrink-src-files: No such file or directory

CDPATH="${ZSH\_VERSION+.}:" && cd . && /bin/sh /home/mroyo/Flexoelectrics/Src/abinit-develop-last/config/gnu/missing aclocal-1.13 -I config/m4

cd . && /bin/sh /home/mroyo/Flexoelectrics/Src/abinit-develop-last/config/gnu/missing automake-1.13 --gnu

CDPATH="${ZSH\_VERSION+.}:" && cd . && /bin/sh /home/mroyo/Flexoelectrics/Src/abinit-develop-last/config/gnu/missing autoconf

/bin/sh ./config.status --recheck

running CONFIG\_SHELL=/bin/sh /bin/sh ./configure --with-config-file=/home/mroyo/.abinit/build/supermat\_gomkl-2020b.ac --no-create --no-recursion

Can anyone help me with this issue?

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<div class="post-metadata">

**Author:** ![fgoudreault](https://discourse.abinit.org/user_avatar/discourse.abinit.org/fgoudreault/32/104_2.png) [@fgoudreault](https://discourse.abinit.org/u/fgoudreault)\
**Post date:** [November 9, 2021, 4:29pm UTC](https://discourse.abinit.org/t/infinite-configure-run-after-executing-make/3029/2 "2021-11-09T16:29:53Z")

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Hello mroyo! Could you please provide the ac9 file you are using and the complete log from both the configure and the make file?

Also when you say that you can’t compile any versions ranging from v8.8 to trunk/develop: do you always encounter the same problem? I believe that the build system have undergo a big change when going from v8 to v9. Thus your problem might be external to the build system itself?

Félix

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**Author:** ![pouillon](https://discourse.abinit.org/user_avatar/discourse.abinit.org/pouillon/32/9_2.png) [@pouillon](https://discourse.abinit.org/u/pouillon)\
**Post date:** [November 9, 2021, 4:36pm UTC](https://discourse.abinit.org/t/infinite-configure-run-after-executing-make/3029/3 "2021-11-09T16:36:47Z")

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YEs, it is important for us to have a look at your config.log. From the error messages you show above, I see that some variables usually detected by the configure script are not properly set or do not exist.

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<div class="post-metadata">

**Author:** ![mroyo](https://discourse.abinit.org/letter_avatar_proxy/v4/letter/m/e95f7d/32.png) [@mroyo](https://discourse.abinit.org/u/mroyo)\
**Post date:** [November 10, 2021, 1:36pm UTC](https://discourse.abinit.org/t/infinite-configure-run-after-executing-make/3029/4 "2021-11-10T13:36:01Z")

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Hello,

> [@fgoudreault](#):
>
> Also when you say that you can’t compile any versions ranging from v8.8 to trunk/develop: do you always encounter the same problem? I believe that the build system have undergo a big change when going from v8 to v9. Thus your problem might be external to the build system itself?

Yes the problem is always the same despite I use different configure flags or .ac files for v8 an v9 versions. I agree that the build system must be OK and here I face a problem with our local configuration. Actually, I can compile these versions of the software in other machines.

I’m trying to upload or paste the .ac and config.log in this message but I can’t because I overpass the characters limit for a new user. Is there any other way to do this?

Thanks for your help.

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<div class="post-metadata">

**Author:** ![fgoudreault](https://discourse.abinit.org/user_avatar/discourse.abinit.org/fgoudreault/32/104_2.png) [@fgoudreault](https://discourse.abinit.org/u/fgoudreault)\
**Post date:** [November 10, 2021, 1:53pm UTC](https://discourse.abinit.org/t/infinite-configure-run-after-executing-make/3029/5 "2021-11-10T13:53:16Z")

</div>

You can upload files I believe. Just press the ![image](https://discourse.abinit.org/uploads/default/original/1X/354891ab6ed848362a4e04d146b902200ac3bd91.png) button when replying to this thread 🙂

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<div class="post-metadata">

**Author:** ![mroyo](https://discourse.abinit.org/letter_avatar_proxy/v4/letter/m/e95f7d/32.png) [@mroyo](https://discourse.abinit.org/u/mroyo)\
**Post date:** [November 10, 2021, 1:58pm UTC](https://discourse.abinit.org/t/infinite-configure-run-after-executing-make/3029/6 "2021-11-10T13:58:00Z")

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I tried but…

Sorry, new users can not upload attachments.

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<div class="post-metadata">

**Author:** ![gmatteo](https://discourse.abinit.org/user_avatar/discourse.abinit.org/gmatteo/32/6_2.png) [@gmatteo](https://discourse.abinit.org/u/gmatteo)\
**Post date:** [November 10, 2021, 2:08pm UTC](https://discourse.abinit.org/t/infinite-configure-run-after-executing-make/3029/7 "2021-11-10T14:08:22Z")

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> Sorry, new users can not upload attachments.

Can you try again?

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<div class="post-metadata">

**Author:** ![mroyo](https://discourse.abinit.org/letter_avatar_proxy/v4/letter/m/e95f7d/32.png) [@mroyo](https://discourse.abinit.org/u/mroyo)\
**Post date:** [November 10, 2021, 2:11pm UTC](https://discourse.abinit.org/t/infinite-configure-run-after-executing-make/3029/8 "2021-11-10T14:11:00Z")

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Ok, I have been updated to moderator. Thanks!

Let’s see. Here it goes the config.log:  
[config.log](https://discourse.abinit.org/uploads/short-url/eNZYNcMz7f6bx4t4GUf3EYXd2YA.log) (305.6 KB)

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<div class="post-metadata">

**Author:** ![mroyo](https://discourse.abinit.org/letter_avatar_proxy/v4/letter/m/e95f7d/32.png) [@mroyo](https://discourse.abinit.org/u/mroyo)\
**Post date:** [November 10, 2021, 2:13pm UTC](https://discourse.abinit.org/t/infinite-configure-run-after-executing-make/3029/9 "2021-11-10T14:13:44Z")

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And here the ac9 file with a .log extension (otherwise it complains):  
[supermat\_gomkl-2020b.ac.log](https://discourse.abinit.org/uploads/short-url/zTZd3uiM64LZpoBEfhKbvHwJCoa.log) (38.2 KB)

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<div class="post-metadata">

**Author:** ![gmatteo](https://discourse.abinit.org/user_avatar/discourse.abinit.org/gmatteo/32/6_2.png) [@gmatteo](https://discourse.abinit.org/u/gmatteo)\
**Post date:** [November 10, 2021, 2:17pm UTC](https://discourse.abinit.org/t/infinite-configure-run-after-executing-make/3029/10 "2021-11-10T14:17:50Z")

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> [@mroyo](#):
>
> And here the ac9 file with a .log extension (otherwise it complains):

Now it’s possible to upload files with extension ac or ac9

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<div class="post-metadata">

**Author:** ![mroyo](https://discourse.abinit.org/letter_avatar_proxy/v4/letter/m/e95f7d/32.png) [@mroyo](https://discourse.abinit.org/u/mroyo)\
**Post date:** [November 12, 2021, 9:20am UTC](https://discourse.abinit.org/t/infinite-configure-run-after-executing-make/3029/11 "2021-11-12T09:20:42Z")

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So, do you have any idea of what is going on?

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<div class="post-metadata">

**Author:** ![jmbgmx](https://discourse.abinit.org/user_avatar/discourse.abinit.org/jmbgmx/32/285_2.png) [@jmbgmx](https://discourse.abinit.org/u/jmbgmx)\
**Post date:** [November 12, 2021, 7:06pm UTC](https://discourse.abinit.org/t/infinite-configure-run-after-executing-make/3029/12 "2021-11-12T19:06:58Z")

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Hi Miquel,

Can you send me the “Final remarks” at the end of ./configure ?

jmb

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<div class="post-metadata">

**Author:** ![mroyo](https://discourse.abinit.org/letter_avatar_proxy/v4/letter/m/e95f7d/32.png) [@mroyo](https://discourse.abinit.org/u/mroyo)\
**Post date:** [November 15, 2021, 7:56am UTC](https://discourse.abinit.org/t/infinite-configure-run-after-executing-make/3029/13 "2021-11-15T07:56:59Z")

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Hi Jean-Michel,

here you have it:

# ============================================================================== === Final remarks ===

## Core build parameters

- C compiler : gnu version 10.2

- Fortran compiler : gnu version 10.2

- architecture : intel xeon (64 bits)

- debugging : basic

- optimizations : standard

- OpenMP enabled : no (collapse: ignored)

- MPI enabled : yes (flavor: auto)

- MPI in-place : no

- MPI-IO enabled : yes

- GPU enabled : no (flavor: none)

- LibXML2 enabled : no

- LibPSML enabled : no

- XMLF90 enabled : no

- HDF5 enabled : yes (MPI support: yes)

- NetCDF enabled : yes (MPI support: yes)

- NetCDF-F enabled : yes (MPI support: yes)

- FFT flavor : dfti (libs: user-defined)

- LINALG flavor : mkl (libs: user-defined)

- SCALAPACK enabled : yes

- ELPA enabled : no

- FCFLAGS : --free-line-length-none -fallow-argument-mismatch -I/share/apps/easybuild/software/netCDF/4.7.4-gompi-2020b/include -I/share/apps/easybuild/software/netCDF-Fortran/4.5.3-gompi-2020b/include

- CPATH : /share/apps/easybuild/software/netCDF-Fortran/4.5.3-gompi-2020b/include:/share/apps/easybuild/software/netCDF/4.7.4-gompi-2020b/include:/share/apps/easybuild/software/cURL/7.72.0-GCCcore-10.2.0/include:/share/apps/easybuild/software/HDF5/1.10.7-gompi-2020b/include:/share/apps/easybuild/software/Szip/2.1.1-GCCcore-10.2.0/include:/share/apps/easybuild/software/libxc/4.3.4-GCC-10.2.0/include:/share/apps/easybuild/software/imkl/2020.4.304-gompi-2020b/mkl/include/fftw:/share/apps/easybuild/software/imkl/2020.4.304-gompi-2020b/mkl/include:/share/apps/easybuild/software/OpenMPI/4.0.5-GCC-10.2.0/include:/share/apps/easybuild/software/PMIx/3.1.5-GCCcore-10.2.0/include:/share/apps/easybuild/software/libfabric/1.11.0-GCCcore-10.2.0/include:/share/apps/easybuild/software/UCX/1.9.0-GCCcore-10.2.0/include:/share/apps/easybuild/software/libevent/2.1.12-GCCcore-10.2.0/include:/share/apps/easybuild/software/hwloc/2.2.0-GCCcore-10.2.0/include:/share/apps/easybuild/software/libpciaccess/0.16-GCCcore-10.2.0/include:/share/apps/easybuild/software/libxml2/2.9.10-GCCcore-10.2.0/include/libxml2:/share/apps/easybuild/software/libxml2/2.9.10-GCCcore-10.2.0/include:/share/apps/easybuild/software/XZ/5.2.5-GCCcore-10.2.0/include:/share/apps/easybuild/software/numactl/2.0.13-GCCcore-10.2.0/include:/share/apps/easybuild/software/binutils/2.35-GCCcore-10.2.0/include:/share/apps/easybuild/software/zlib/1.2.11-GCCcore-10.2.0/include

- Build workflow : monolith

0 deprecated options have been used:.

Configuration complete.  
You may now type “make” to build Abinit.  
(or “make -j”, where is the number of available processors)

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<div class="post-metadata">

**Author:** ![pouillon](https://discourse.abinit.org/user_avatar/discourse.abinit.org/pouillon/32/9_2.png) [@pouillon](https://discourse.abinit.org/u/pouillon)\
**Post date:** [November 15, 2021, 10:38am UTC](https://discourse.abinit.org/t/infinite-configure-run-after-executing-make/3029/14 "2021-11-15T10:38:30Z")

</div>

I’ve found some comments about a similar problem in the past and it was due to the Python interpreter not found properly. There are 2 workarounds:

- Set the PYTHON environment variable to the full path of a Python 3 interpreter;
- Install the `python-is-python3` package on Debian-based distributions.

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<div class="post-metadata">

**Author:** ![pouillon](https://discourse.abinit.org/user_avatar/discourse.abinit.org/pouillon/32/9_2.png) [@pouillon](https://discourse.abinit.org/u/pouillon)\
**Post date:** [November 15, 2021, 10:41am UTC](https://discourse.abinit.org/t/infinite-configure-run-after-executing-make/3029/15 "2021-11-15T10:41:51Z")

</div>

Be careful that the second suggestion may interfere with external legacy scripts depending on Python 2, if you still rely on outdated implementations for other projects than ABINIT. This should not be a problem for most people, though.

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<div class="post-metadata">

**Author:** ![mroyo](https://discourse.abinit.org/letter_avatar_proxy/v4/letter/m/e95f7d/32.png) [@mroyo](https://discourse.abinit.org/u/mroyo)\
**Post date:** [November 15, 2021, 6:38pm UTC](https://discourse.abinit.org/t/infinite-configure-run-after-executing-make/3029/16 "2021-11-15T18:38:14Z")

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Hello @pouillon

do you think it suffices to create an alias for python pointing to python3? I have tried this option and the problem persists.

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<div class="post-metadata">

**Author:** ![pouillon](https://discourse.abinit.org/user_avatar/discourse.abinit.org/pouillon/32/9_2.png) [@pouillon](https://discourse.abinit.org/u/pouillon)\
**Post date:** [November 16, 2021, 10:51am UTC](https://discourse.abinit.org/t/infinite-configure-run-after-executing-make/3029/17 "2021-11-16T10:51:25Z")

</div>

Installing the `python-is-python3` package does a little bit more than that, thus I don’t know if an alias will solve everything. If you do that, you should also alias `python3-config`.

Thinking again about this topic, there is a third alternative, which consists in configuring ABINIT in an activated Python virtual environment. Depending on your distribution, you may have to install the `python3-venv` package first.

E.g.:

```auto
/usr/bin/python3 -m venv ~/my-envs/abinit
source ~/my-envs/abinit/bin/activate
../configure ...

```

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<div class="post-metadata">

**Author:** ![mroyo](https://discourse.abinit.org/letter_avatar_proxy/v4/letter/m/e95f7d/32.png) [@mroyo](https://discourse.abinit.org/u/mroyo)\
**Post date:** [November 16, 2021, 11:31am UTC](https://discourse.abinit.org/t/infinite-configure-run-after-executing-make/3029/18 "2021-11-16T11:31:10Z")

</div>

Thanks for the suggestion. I have activated the virtual environment as :

> [@pouillon](#):
>
> ```auto
> /usr/bin/python3 -m venv ~/my-envs/abinit
> source ~/my-envs/abinit/bin/activate
> 
> ```

but even then, the problem persists )-:

Do you know if it might be a question of using an old version of “make”? I have noticed that the one in the cluster is v3.82, whereas the one in my PC (wherein I can build abinit with no problems) is v4.2.1.

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<div class="post-metadata">

**Author:** ![mroyo](https://discourse.abinit.org/letter_avatar_proxy/v4/letter/m/e95f7d/32.png) [@mroyo](https://discourse.abinit.org/u/mroyo)\
**Post date:** [November 16, 2021, 11:52am UTC](https://discourse.abinit.org/t/infinite-configure-run-after-executing-make/3029/19 "2021-11-16T11:52:23Z")

</div>

Actually, I have realized that the configure detects python3.6 but not python3.6-config:

checking for python3.6… python3.6  
checking for python3.6-config… no  
checking for python3.7-config… no  
checking for python3.6-config… no  
checking for python3.5-config… no  
checking for python3.4-config… no  
checking for python3-config… no  
checking for python2.7-config… python2.7-config

So that maybe it is still a question of setting the python3 environment properly.

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<div class="post-metadata">

**Author:** ![pouillon](https://discourse.abinit.org/user_avatar/discourse.abinit.org/pouillon/32/9_2.png) [@pouillon](https://discourse.abinit.org/u/pouillon)\
**Post date:** [November 16, 2021, 3:38pm UTC](https://discourse.abinit.org/t/infinite-configure-run-after-executing-make/3029/20 "2021-11-16T15:38:21Z")

</div>

What happens if you do this?

```auto
sudo apt install python3-dev

```

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