Build subdirectory cannot be created on Ubuntu18.04

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xiongyan21
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Build subdirectory cannot be created on Ubuntu18.04

Post by xiongyan21 » 11 Feb 2019, 05:17

I followed the direaction on the forum to git clone DALTON, but when I ran "cd build" after "setup --help", build directory had not been created.
The default git clone version is 2019 alpha.
What is the problem here and how can I get 2018 version?
Which should I choose after "git checkout 2018.0"?
Thanks!

Very Best Regards!

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magnus
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Re: Build subdirectory cannot be created on Ubuntu18.04

Post by magnus » 11 Feb 2019, 10:15

Assuming you cloned the repository using the following command:

Code: Select all

git clone --recursive https://gitlab.com/dalton/dalton.git
You can checkout the latest released version using the command:

Code: Select all

git checkout Dalton2018.0
and then update submodules by:

Code: Select all

git submodule update
Then you can build the code as follows:

Code: Select all

./setup
cd build
make
The options shown in square brackets are optional, so the command:

Code: Select all

./setup [--help]
means that --help is optional. This option will show you how to use the setup script and not actually do anything.

xiongyan21
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Re: Build subdirectory cannot be created on Ubuntu18.04

Post by xiongyan21 » 11 Feb 2019, 14:04

Dear Prof. Olsen
Actually, the error was caused by the missing of cmake, after it had been installed, Dalton is successfully built.
The command git checkout DAlton2018.0 showed
error: 您对下列文件的本地修改将被检出操作覆盖:
.codecov.yml
.gitlab-ci.yml
CHANGELOG.md
DALTON/Doc/Master.tex
DALTON/Doc/Sirius.tex
DALTON/Doc/embedding.tex
DALTON/cc/crayio.c
DALTON/dft/basisinfo.c
DALTON/dft/fun-cam-b3lyp.c
DALTON/dft/fun-gga.c
DALTON/dft/fun-rcam-b3lyp.c
DALTON/dft/functionals.c
DALTON/dft/general.c
DALTON/dft/general.h
DALTON/dft/quad-faster.c
DALTON/fde/emb_export.F90
DALTON/gen1int/gen1int_api.F90
DALTON/gen1int/gen1int_cube.F90
DALTON/gen1int/gen1int_host.F90
DALTON/gen1int/gen1int_matrix.F90
DALTON/gen1int/gen1int_shell.F90
DALTON/sirius/sirinp.F
DALTON/sirius/sirmp2.F
DALTON/sirius/sirntra.F
DALTON/sirius/siropt.F
DALTON/sirius/sirstex.F
DALTON/test/dft_ac_multpole/OC-ClF_A.dal
DALTON/test/dft_ac_multpole/OC-ClF_A.mol
VERSION
cmake/TestsDALTON.cmake
cmake/binary-info/ConfigGitRevision.cmake
cmake/compilers/FortranFlags.cmake
请在切换分支前提交或贮藏您的修改。
终止中
The command git submodule update gave nothing

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magnus
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Re: Build subdirectory cannot be created on Ubuntu18.04

Post by magnus » 11 Feb 2019, 14:40

The reason it fails is because you have local changes in those files, so if you were to change branch or checkout a tag those changes would be overwritten. You can check the current status using the command: git status

xiongyan21
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Re: Build subdirectory cannot be created on Ubuntu18.04

Post by xiongyan21 » 11 Feb 2019, 15:20

Dear Prof. Olsen
The previously compiled Dalton using ctest -j4 made all the other tests pass except the following
2 - dft_ac_multpole (Failed)
3 - dft_b3lyp_cart (Failed)
80 - geoopt_prop3_ex (Failed)
488 - benchmark_eri_adz (Timeout)
490 - benchmark_eri_atzs (Timeout)
492 - benchmark_eri_r12xl (Timeout)
493 - benchmark_her_adz (Timeout)
495 - benchmark_her_atzs (Timeout)

I will try git status.

Very Best Regards!

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magnus
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Re: Build subdirectory cannot be created on Ubuntu18.04

Post by magnus » 11 Feb 2019, 15:24

Ok, you are using the master branch which is for development so it can happen that some tests fail. For instance the dft_ac_multpole fails because of a known bug.

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Re: Build subdirectory cannot be created on Ubuntu18.04

Post by xiongyan21 » 12 Feb 2019, 08:38

I haved used three commands you suggested, but still got
...
2 - dft_ac_multpole (Failed)
3 - dft_b3lyp_cart (Failed)
80 - geoopt_prop3_ex (Failed)
488 - benchmark_eri_adz (Timeout)
489 - benchmark_eri_adzs (Timeout)
490 - benchmark_eri_atzs (Timeout)
492 - benchmark_eri_r12xl (Timeout)
493 - benchmark_her_adz (Timeout)
495 - benchmark_her_atzs (Timeout)
Errors while running CTest
It seems I cannot download DAlton2018.0 in this way, because it is still the developmental version 2019 alpha.

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magnus
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Re: Build subdirectory cannot be created on Ubuntu18.04

Post by magnus » 12 Feb 2019, 09:03

And the reason is that some files are changed. Now I don't know if those changes have been made intentionally or not, so I'm hesitant to make any recommendations about what you can do with those changes. The only recommendation I have is that you try from a fresh clone, checking out the latest release at the same time. You can do this with the following series of commands:

Code: Select all

git clone --recursive -b Dalton2018.1 https://gitlab.com/dalton/dalton.git Dalton2018
cd Dalton2018
./setup
cd build
make
Note that this will create a new clone of the repository in a Dalton2018 directory.

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Re: Build subdirectory cannot be created on Ubuntu18.04

Post by xiongyan21 » 12 Feb 2019, 11:55

Dear Prof. Olsen
I followed you to reclone and build Dalton2018,1, issued in 2019, and found the following using ctest -j4
...
The following tests FAILED:
2 - dft_b3lyp_cart (Failed)
79 - geoopt_prop3_ex (Failed)
487 - benchmark_eri_adz (Timeout)
488 - benchmark_eri_adzs (Timeout)
489 - benchmark_eri_atzs (Timeout)
491 - benchmark_eri_r12xl (Timeout)
492 - benchmark_her_adz (Timeout)
493 - benchmark_her_adzs (Timeout)
494 - benchmark_her_atzs (Timeout)
Errors while running CTest

I also found actually test 2 and 9 already finished faster than the original example with the same results although they were labelled failed in the terminal. I reran them and found they all could finish with the identical results with those in the accompanying test clips, respectively.

There is one thing unusual, i.e., although mpi is off, command mpirun works. I think I might export mpi and recompile.

I used mpirun to calculate the new cc(T) test benchmark_eri_adz, and got the following
...
Perturbative triples corrections
--------------------------------

The E4 doubles and triples: ...
The E5 singles and triples: ...

Total energy CCSD(T): ...


*******************************************************************************
*******************************************************************************
* *
* *
* END OF COUPLED CLUSTER CALCULATION *
* *
* *
*******************************************************************************
*******************************************************************************


CPU and wall time for CC : ...


Date and time (Linux) : ...
Host name : ...

.-------------------------------------.
| End of Coupled Cluster Section (CC) |
`-------------------------------------'

Total CPU time used in DALTON: ...
Total wall time used in DALTON: ...

Date and time (Linux) : ...
Host name : ...

Very Best Regards!
Last edited by xiongyan21 on 14 Feb 2019, 04:06, edited 5 times in total.

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magnus
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Re: Build subdirectory cannot be created on Ubuntu18.04

Post by magnus » 12 Feb 2019, 13:18

I wouldn't worry about the benchmark tests since they are just timing out and not failing as such. You could look into the other two tests to see why they are failing. The outputs from the tests are in the tests directory in your build directory.

Not sure I understand what is the issue with MPI. Even if you didn't compile with MPI, you can still run an executable using mpirun but it will not make sense. Note also that CC is not MPI parallelized.

xiongyan21
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Re: Build subdirectory cannot be created on Ubuntu18.04

Post by xiongyan21 » 12 Feb 2019, 13:32

Dear Prof. Olsen
The other two actually have been successful altough they were labelled failed during ctest -j4.

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magnus
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Re: Build subdirectory cannot be created on Ubuntu18.04

Post by magnus » 12 Feb 2019, 13:39

Great. Good luck with your calculations :-)

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