"Non-zero exit code detected." when compile cp2k 7.1

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Jiayu Sun SLE

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Jun 10, 2020, 11:08:21 PM6/10/20
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Hi, everyone,
I have tried compiled the cp2k 7.1 version from toolchain script, the *sh file, and using the OpenBLAS 0.3.6, the error message are listed below:

==================== Installing OpenBLAS ====================
OpenBLAS-0.3.6.tar.gz is found
Installing from scratch into /home/jiayusun/Downloads/cp2k-7.1/tools/toolchain/install/openblas-0.3.6
patching file kernel/x86_64/KERNEL.SKYLAKEX
ERROR: (/home/jiayusun/Downloads/cp2k-7.1/tools/toolchain/scripts/install_openblas.sh, line 72) Non-zero exit code detected.
ERROR: (./scripts/install_mathlibs.sh, line 34) Non-zero exit code detected.


How can I do this in this case?
What the meaning of this sentence: "Non-zero exit code detected." When I compile other packages, this error occurs again, almost all the packages are facing the same problem.

Thank you for your help or advice.

Sincerely

Anton S. Lytvynenko

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Jun 11, 2020, 6:26:36 AM6/11/20
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11.06.20 06:08, Jiayu Sun SLE пише:

Installing from scratch into /home/jiayusun/Downloads/cp2k-7.1/tools/toolchain/install/openblas-0.3.6
patching file kernel/x86_64/KERNEL.SKYLAKEX
ERROR: (/home/jiayusun/Downloads/cp2k-7.1/tools/toolchain/scripts/install_openblas.sh, line 72) Non-zero exit code detected.
ERROR: (./scripts/install_mathlibs.sh, line 34) Non-zero exit code detected.


How can I do this in this case?
What the meaning of this sentence: "Non-zero exit code detected." When I compile other packages, this error occurs again, almost all the packages are facing the same problem.

Hi,

When the program ends, it returns so called exit code -- an integer value indicating if it was successful. By convention, exit code 0 means successful execution, non-integer ones typically indicate some issues (they can have their own conventions depending on the system or software, but such conventions are more specific). The sentence you are citing means that the install_openblas.sh script failed for some reason. I guess your system misses some packages necessary to build the code, and you should figure out which ones and install them. Please check the logs on the openblas build (see "[CP2K:10684] installation of cp2k on linux mint machine" topic for similar situation and discussion how to find them).

Yours,

Anton

Anton S. Lytvynenko

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Jun 11, 2020, 7:13:42 AM6/11/20
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By the way, did you run sudo ./install_requirements.sh first?

11.06.20 06:08, Jiayu Sun SLE пише:
Hi, everyone,
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Jiayu Sun SLE

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Jun 12, 2020, 9:01:19 AM6/12/20
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Hi Anton

Thank you for you kindly help. I haven't run the install_requirements.sh first. After running it, the screen printed:


Selecting previously unselected package libopts25:amd64.
(Reading database ... 186821 files and directories currently installed.)
Preparing to unpack .../00-libopts25_1%3a5.18.16-3_amd64.deb ...
Unpacking libopts25:amd64 (1:5.18.16-3) ...
Selecting previously unselected package libopts25-dev:amd64.
Preparing to unpack .../01-libopts25-dev_1%3a5.18.16-3_amd64.deb ...
Unpacking libopts25-dev:amd64 (1:5.18.16-3) ...
Selecting previously unselected package autogen.
Preparing to unpack .../02-autogen_1%3a5.18.16-3_amd64.deb ...
Unpacking autogen (1:5.18.16-3) ...
Replaced by files in installed package libopts25-dev:amd64 (1:5.18.16-3) ...
Selecting previously unselected package liberror-perl.
Preparing to unpack .../03-liberror-perl_0.17029-1_all.deb ...
Unpacking liberror-perl (0.17029-1) ...
Selecting previously unselected package git-man.
Preparing to unpack .../04-git-man_1%3a2.25.1-1ubuntu3_all.deb ...
Unpacking git-man (1:2.25.1-1ubuntu3) ...
Selecting previously unselected package git.
Preparing to unpack .../05-git_1%3a2.25.1-1ubuntu3_amd64.deb ...
Unpacking git (1:2.25.1-1ubuntu3) ...
Selecting previously unselected package libblas3:amd64.
Preparing to unpack .../06-libblas3_3.9.0-1build1_amd64.deb ...
Unpacking libblas3:amd64 (3.9.0-1build1) ...
Selecting previously unselected package liblapack3:amd64.
Preparing to unpack .../07-liblapack3_3.9.0-1build1_amd64.deb ...
Unpacking liblapack3:amd64 (3.9.0-1build1) ...
Selecting previously unselected package make.
Preparing to unpack .../08-make_4.2.1-1.2_amd64.deb ...
Unpacking make (4.2.1-1.2) ...
Selecting previously unselected package python-pkg-resources.
Preparing to unpack .../09-python-pkg-resources_44.0.0-2_all.deb ...
Unpacking python-pkg-resources (44.0.0-2) ...
Selecting previously unselected package python-numpy.
Preparing to unpack .../10-python-numpy_1%3a1.16.5-2ubuntu7_amd64.deb ...
Unpacking python-numpy (1:1.16.5-2ubuntu7) ...
Selecting previously unselected package zlib1g-dev:amd64.
Preparing to unpack .../11-zlib1g-dev_1%3a1.2.11.dfsg-2ubuntu1_amd64.deb ...
Unpacking zlib1g-dev:amd64 (1:1.2.11.dfsg-2ubuntu1) ...
Setting up python-pkg-resources (44.0.0-2) ...
Setting up libopts25:amd64 (1:5.18.16-3) ...
Setting up liberror-perl (0.17029-1) ...
Setting up libblas3:amd64 (3.9.0-1build1) ...
update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode
Setting up make (4.2.1-1.2) ...
Setting up zlib1g-dev:amd64 (1:1.2.11.dfsg-2ubuntu1) ...
Setting up git-man (1:2.25.1-1ubuntu3) ...
Setting up liblapack3:amd64 (3.9.0-1build1) ...
update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode
Setting up python-numpy (1:1.16.5-2ubuntu7) ...
Setting up libopts25-dev:amd64 (1:5.18.16-3) ...
Setting up autogen (1:5.18.16-3) ...
Setting up git (1:2.25.1-1ubuntu3) ...
Processing triggers for libc-bin (2.31-0ubuntu9) ...
Processing triggers for man-db (2.9.1-1) ...
Processing triggers for install-info (6.7.0.dfsg.2-5) ...

I cannot figure out what I should do next, what's the meaning of these codes?
Does this message show the missing package I should install but not yet?

Thank you so much.
SUN

在 2020年6月11日星期四 UTC+9下午12:08:21,Jiayu Sun SLE写道:

Anton S. Lytvynenko

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Jun 12, 2020, 10:44:39 AM6/12/20
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Hi,

12.06.20 16:01, Jiayu Sun SLE пише:
> I cannot figure out what I should do next, what's the meaning of these
> codes?

These codes report a successful installation of the necessary packages.

Besides some specific staff shipped together with CP2K, the program
relies on a number of additional common software necessary to build the
binaries -- namely, compilers, libraries, building systems etc. This
software comes from your distribution, but some of them are not
installed by default -- so, they are accessible from the repository, but
must be installed explicitly. That script (install_requirements.sh) just
forces your system to install missing packages (via APT manager, i.e. by
a conventional way employed in Ubuntu/Mint/Debian).

After that, you can return to install_cp2k_toolchain.sh script -- now it
should proceed without errors.

Anton

Jiayu Sun SLE

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Jun 12, 2020, 2:44:15 PM6/12/20
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Hi Anton
Thank you for your kindly help and patience.

Now, I installed some packages and rerun the sh script and almost all the packages are installed, then the code skips, but only two packages shows error message, I print here:

==================== Installing ScaLAPACK ====================
scalapack-2.0.2.tgz is found
Installing from scratch into /home/jiayusun/Downloads/cp2k-7.1/tools/toolchain/install/scalapack-2.0.2
ERROR: (./scripts/install_scalapack.sh, line 47) Non-zero exit code detected.
==================== Installing ELPA ====================
elpa-2019.05.001.tar.gz is found
Installing from scratch into /home/jiayusun/Downloads/cp2k-7.1/tools/toolchain/install/elpa-2019.05.001
ERROR: (./scripts/install_elpa.sh, line 84) Non-zero exit code detected.
Step ptscotch took 0.00 seconds.
Step parmetis took 0.00 seconds.
Step metis took 0.00 seconds.
Step superlu took 0.00 seconds.
Step pexsi took 0.00 seconds.
Step quip took 0.00 seconds.
Step plumed took 0.00 seconds

I tried to install Scalapack by myself, before that, the packages of blas,  lapcak, cblas are all installed successfully, but the installation of Scalapack failed eventually.
It's a tough way, now only two packages left, can you give me some advice?

Thank you so much!!


在 2020年6月11日星期四 UTC+9下午12:08:21,Jiayu Sun SLE写道:
Hi, everyone,

Антон Л.

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Jun 13, 2020, 3:32:38 PM6/13/20
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Hi,

first of all, please decide if you really need ScaLAPACK -- or, more generally, if you really need MPI parallelization at all (AFAIK both ScaLAPACK and ELPA depend on MPI). If you plan to run CP2K on a single regular desktop, then you can safely avoid MPI employing only OpenMP parallelization -- I wonder if you could gain any performance profit via MPI over OpenMP.

If so, just disable MPI by running ./install_cp2k_toolchain.sh --mpi-mode=no

Otherwise, if you believe that you indeed want MPI parallelization, e.g. you intend to run the code on a cluster node or on a few desktops connected by network, then you should enter build/scalapack-2.0.2 subfolder and inspect all files with .log extension. Details of any errors should be reported there.

Hope this helps.


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Jiayu Sun

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Jun 14, 2020, 7:38:58 PM6/14/20
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Hi,

Thank you for your reply. I understand the situation.
For now, I mainly use it on my PC, so maybe the two packages are no needed.

Thank you again.
Sincerely





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Антон Л. <tenebrosu...@gmail.com> 于2020年6月14日周日 上午4:32写道:
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