Installation Problem

cymantren · 2017-09-19 11:07:58

Hello everybody,

I am a new OPENMOLCAS-User and try to install the program via cmake as described on this site: https://gitlab.com/Molcas/OpenMolcas.
Everything went fine until the "4. make". I finished it, because it did'nt continued for hours.
The make.log message is partly:

.................
100%] Built target casvb.exe
Scanning dependencies of target pymolcas
[100%] Generating pymolcas_
pymolcas will be installed in /home/Kernel07/bin
Is this OK? [Y/n] (will assume "Yes" in 25 seconds)
CMakeFiles/Makefile2:7290: recipe for target 'Tools/pymolcas/CMakeFiles/pymolcas.dir/all' failed

Of course, first time I typed "Y" and the second time I waited, because "will assume "Yes" in 25 seconds". But nothing happened for hours !
How do I verify and finish the installation? It is more sensible to use "ccmake .." ?

Thank you in advance for answering !

kindly regards

Alfred Güthler

Ignacio · 2017-09-19 19:19:30

Somehow the install_pymolcas.sh script is not doing what it should. Try manually running:

cp Tools/pymolcas/pymolcas_ /home/Kernel07/bin/pymolcas

(note the underscore in the first file and not the second)

cymantren · 2017-09-20 09:16:24

Dear Ignacio,

thank you for your reply -it worked!
How do I start a calculation, e.g. 000.input ? I tried but received:

Traceback (most recent call last):
  File "/home/Kernel07/bin/pymolcas", line 355, in <module>
    exec('import zlib,base64;exec(zlib.decompress(base64.b64decode(m[1])),module.__dict__);del zlib,base64')
  File "<string>", line 1, in <module>
  File "<string>", line 19, in <module>
ImportError: No module named 'pyparsing'

According to the manual 3.1.2 "Molcas Environment Setup", I made the following adjustments at my ".bashrc"-script:

export MOLCAS=/home/Kernel07/OpenMolcas/ ????
export PATH=$PATH:$HOME/bin

However the error message remains. Do I have to make/correct further adjustments ?

Thank you in advance for your answer.

best greetings

Alfred Güthler

Ignacio · 2017-09-20 23:21:52

You need the pyparsing module for python. The Molcas manual is alright, but it hasn't been updated for the OpenMolcas specifics (most of it should still be valid, though). Check the wiki: https://gitlab.com/Molcas/OpenMolcas/wi … ck%20start

cymantren · 2017-09-21 12:11:19

Dear Ignacio,

your suggestion in principle worked, however this time I get:

 "/home/Kernel07/OpenMolcas" is not a valid MOLCAS installation

I suppose, I just have to change "Molcas" <--> "OpenMolcas" but where ?

Please help me.
Moreover I also ask for a principle help, namly the differerence in the "Molcas" instructions and "OpenMolcas". You said, that most of the instructions work for both programs, but how do one knows, if it doesn't work in advance ? The manual says that, programs which don't work with OpenMolcas are marked.

kindly regards

Alfred Güthler

Ignacio · 2017-09-21 14:59:38

cymantren wrote:

your suggestion in principle worked, however this time I get:
 "/home/Kernel07/OpenMolcas" is not a valid MOLCAS installation
I suppose, I just have to change "Molcas" <--> "OpenMolcas" but where ?

No, it's not a problem of "OpenMolcas" vs. "Molcas".

Make sure you "export MOLCAS" line points to the build or installation directory, not to the source directory. If you run "make install" you shouldn't need to manually set the MOLCAS variable, since it is written in the configuration file.

Moreover I also ask for a principle help, namly the differerence in the "Molcas" instructions and "OpenMolcas". You said, that most of the instructions work for both programs, but how do one knows, if it doesn't work in advance ? The manual says that, programs which don't work with OpenMolcas are marked.

You can't know, because the documentation is not 100% up to date. This has always been a problem, but with the release of OpenMolcas it may be more evident in some points. Regarding the programs which are not available in OpenMolcas, they are marked with a sign in the documentation. for instance CMOCORR or DIMERPERT. Anyway, the differences between OpenMolcas and Molcas are only in compilation/configuration/infrastructure and the availability of some programs or features. The programs available in both (e.g. RASSCF) work exactly the same.

cymantren · 2017-09-26 10:50:35

Dear Ignacio,

There are still 2 Problems.

A) I installed different libraries, hdf5-openmpi, MKL-2018.0.128 and pyparsing, configured via "ccmake .." , "cmake" , which both works ! However "make > make log &" gives:

..............
[ 70%] Building Fortran object CMakeFiles/alaska.exe.dir/src/alaska/main.f.o
Linking Fortran executable bin/alaska.exe
CMakeFiles/alaska.exe.dir/build.make:120: recipe for target 'bin/alaska.exe' failed
CMakeFiles/Makefile2:143: recipe for target 'CMakeFiles/alaska.exe.dir/all' failed
Makefile:117: recipe for target 'all' failed

B) A test at $HOME/bin/000input/ gives:

pymolcas 000.input
  File "/home/kernel9-16/bin/pymolcas", line 20
    molcas_aux', '''
                 ^
SyntaxError: invalid syntax

There are still some errors!
But on my old laptop (also debian jessie), OpenMolcas at least works, but "make > make.log" gives the same error message.

I wonder what is still wrong, because I think I did the neccessary adjustments at ".bashrc".

Can you figure out what still goes wrong ?

Thank you for your answers and help !

kind greetings

Alfred Güthler

Ignacio · 2017-09-26 14:53:28

cymantren wrote:

A) I installed different libraries, hdf5-openmpi, MKL-2018.0.128 and pyparsing, configured via "ccmake .." , "cmake" , which both works ! However "make > make log &" gives:
..............
[ 70%] Building Fortran object CMakeFiles/alaska.exe.dir/src/alaska/main.f.o
Linking Fortran executable bin/alaska.exe
CMakeFiles/alaska.exe.dir/build.make:120: recipe for target 'bin/alaska.exe' failed
CMakeFiles/Makefile2:143: recipe for target 'CMakeFiles/alaska.exe.dir/all' failed
Makefile:117: recipe for target 'all' failed

That is not very informative. There may be some other error further up, or you may get more info with "make VERBOSE=1 > make.log". Otherwise I have no idea.

B) A test at $HOME/bin/000input/ gives:

pymolcas 000.input
  File "/home/kernel9-16/bin/pymolcas", line 20
    molcas_aux', '''
                 ^
SyntaxError: invalid syntax

Which python version are you using? ("python3 --version") It could be that some earlier or later version is required. That line in pymolcas should be:

  ['molcas_aux', '''

so something is missing

cymantren · 2017-09-29 12:33:43

Hello Mr. Ignacio,

THE INSTALLATION PROBLEM IS SOLVED.

I finally succeeded in installing OPENMOLCAS on my debian-jessie system and ran "pymolcas verify". The result was that of the 897 test files, the following files, were skipped or failed:
-------------------------------------------------------------------------------
1Skipped!:standard:013,065,071,205,219

2:additional:205,219 Skipped!!

The "GRAYZONE"-files are expected to fail-at the first run.

3:grayzone:098 Failed! (scf)
3:grayzone:394 Failed! (rasscf)
3:grayzone:395 Failed! (rasscf)
3:grayzone:396 Failed! (rasscf)
3:grayzone:405 Failed! (scf)
3:grayzone:803 Failed! (seward)
3:grayzone:804 Failed! (scf)
3:grayzone:819 Failed! (seward)
3:grayzone:832 Failed! (scf)
3:grayzone:834 Skipped!
3:grayzone:835 Skipped!3:grayzone:850 Failed! (rasscf)
3:grayzone:851 Failed! (rasscf)
3:grayzone:897 Failed! (rasscf)

*Failed critical tests* 0
-----------------------------------------------------------------------------------

I did the following in this order:
1) I installed the neccessary libaries: hdf5,pthon(3)-dev and pyparsing
2) changed the .bashrc:

#OpenMolcas
export MOLCAS=/home/kernel9-16/OpenMolcas/build
export PATH=$PATH:$HOME/bin

3) I
- installed the OpenMolcas-system according to: https://gitlab.com/Molcas/OpenMolcas
---did not use "ccmake ..", acml5.3.1 or MKL-2018
4) After "make > make.log" an error message was produced at the end ;
I used "kill -9 processes 1,2..."
5) Copied the generated pymolcas script at ../tools/pymolcas/pymolcas to /home//bin/
5a) From there I started the above mentioned "pymolcas verify" script
-----------------------------------------------------------------------------------------------------------------------------------
It seems that changing the order of the installation, produces the already mentioned error-messages ! ?

-The Program runs with one core. How can I increase it ?
-There are different additional programs and libraries, e.g.CheMPS2, ACML-5.3.1 and MKL-2018. How can these made available to OPENMOLCAS ?

Thank you for your valuable help !

best greetings

Alfred Güthler

Ignacio · 2017-09-29 17:03:26

cymantren wrote:

-The Program runs with one core. How can I increase it ?

Check https://gitlab.com/Molcas/OpenMolcas/wi … lelization and http://molcas.gitlab.io/doc/sphinx/inst … ainst.html

-There are different additional programs and libraries, e.g.CheMPS2, ACML-5.3.1 and MKL-2018. How can these made available to OPENMOLCAS ?

Those are external programs or libraries. You should (if you want them) get/compile/install them separately, OpenMolcas simply includes and in the case of the math libraries allows linking to them instead of the internal code. The links to the relevant sites are given in https://gitlab.com/Molcas/OpenMolcas/wi … ck%20start

Molcas Forum

Announcement

#1 2017-09-19 11:07:58

Installation Problem

#2 2017-09-19 19:19:30

Re: Installation Problem

#3 2017-09-20 09:16:24

Re: Installation Problem

#4 2017-09-20 23:21:52

Re: Installation Problem

#5 2017-09-21 12:11:19

Re: Installation Problem

#6 2017-09-21 14:59:38

Re: Installation Problem

#7 2017-09-26 10:50:35

Re: Installation Problem

#8 2017-09-26 14:53:28

Re: Installation Problem

#9 2017-09-29 12:33:43

Re: Installation Problem

#10 2017-09-29 17:03:26

Re: Installation Problem

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