gaussiantoqmc test

General discussion of the Cambridge quantum Monte Carlo code CASINO; how to install and setup; how to use it; what it does; applications.
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Bruno_Cramer
Posts: 4
Joined: Sun Dec 22, 2013 3:48 pm

gaussiantoqmc test

Post by Bruno_Cramer »

Hi,
> testing 'gaussiantoqmc c2h2.out c2h2.fchk' I've got

Wrapper failed to find gaussiantoqmc for CASINO_ARCH=linuxpc-ifort-lam-parallel .
Try typing 'make' under CASINO/utils .
-----------------------------------------------
Results obtained after 'make':

bcramer@linux-1bj8:~/CASINO/utils> make
CASINO utils MAKE information
* LN = ln -s
* F90 = ifort -O3 -no-prec-div -no-prec-sqrt -funroll-loops -no-fp-port -ip
-complex-limited-range -par-report0 -vec-report0 -assume protect_parens
-diag-disable 5140 -diag-disable 10010
LDF90 utils > blip
ld: cannot find -llammpio
ld: cannot find -llamf77mpi
ld: cannot find -lmpi
ld: cannot find -llam
make[1]: *** [/home/bcramer/CASINO/utils/wfn_converters/pw_to_blips/../../../bin_qmc/utils/linuxpc-ifort-lam-parallel/blip] Error 1
make: *** [/home/bcramer/CASINO/utils/../bin_qmc/utils/linuxpc-ifort-lam-parallel/blip] Error 1

********************************
Above mentioned missing lib`s are all present in the /mpi-lam/64lib directory and specified in my path:
export LD_LIBRARY_PATH=/usr/local/lam-mpi/lib64

How can this be fixed?
*********************************

Thank you for your help
Regards
Bruno
--------------
PS.
My environment variables

#----------------INTEL Compiler FORTRAN
PATH=$PATH:/opt/intel/composer_xe_2013/bin
PATH=$PATH:/opt/intel/composer_xe_2011_sp1/bin

#--------------------QMC--CASINO

PATH=$PATH:/home/bcramer/CASINO/bin_qmc
export CASINO_ARCH='linuxpc-ifort'

#-----------------------VMD
PATH=$PATH:/usr/local/vmd-1.9.1/bin

#------------------LAM-MPI
PATH=$PATH:/usr/local/lam-mpi/bin
export LD_LIBRARY_PATH=/usr/local/lam-mpi/lib64
export PATH
********************************************************************
Mike Towler
Posts: 239
Joined: Thu May 30, 2013 11:03 pm
Location: Florence
Contact:

Re: gaussiantoqmc test

Post by Mike Towler »

Hi Bruno,

Sorry to hear you're having problems.

So you're having problems trying to run utilities because they failed to compile properly.

Before I investigate:

(1) which version of the code are you trying to install? (presumably 2.12.1 or the current beta?)

(2) how did you install it i.e. is this a manual install or did you use the install script? In either case, could you summarize what you did..

(3) how did you compile it? (manually by typing 'make' in the CASINO base directory, or by using the compile option of the install script?). Presumably it failed to compile the utils properly the first time you did it and you didn't notice? (The 'make utils' thing when you tried to run gaussiantoqmc is a later red herring..).

(4) You're using a pre-existing CASINO_ARCH = linuxpc-ifort-lam-parallel. Are you sure that everything defined in CASINO/arch/data/linuxpc-ifort-lam-parallel.arch (and in all the subfiles it includes) are appropriate for your machine?

M.
Mike Towler
Posts: 239
Joined: Thu May 30, 2013 11:03 pm
Location: Florence
Contact:

Re: gaussiantoqmc test

Post by Mike Towler »

Above mentioned missing lib`s are all present in the /mpi-lam/64lib directory and specified in my path:
export LD_LIBRARY_PATH=/usr/local/lam-mpi/lib64
And presumably the fact that lam-mpi/lib64 is not the same as mpi-lam/64lib is just a typo in your post?

M.
Bruno_Cramer
Posts: 4
Joined: Sun Dec 22, 2013 3:48 pm

Re: gaussiantoqmc test

Post by Bruno_Cramer »

Hi Mike,
I re-installed the program. So consider the answers bellow and also the text of the second installation trial.
(1) which version of the code are you trying to install?
A.: 2.12.1

(2) how did you install it i.e. is this a manual install or did you
use the install script?
In either case, could you summarize what you did..
A.: I reinstalled CASINO as follows:
./install (Automatic) however, before this in my .bashrc I specified 'export linuxpc-ifort-lam-parallel' followed by 'source'

(3) how did you compile it? (manually by typing 'make' in the CASINO base directory,
or by using the compile option of the install script?).
Presumably it failed to compile the utils properly the first time you did it and
you didn't notice? (The 'make utils' thing when you tried to run gaussiantoqmc is a later red herring..).
A.: Automatic as mentioned above.Make was used according to the installation remark

(4) You're using a pre-existing CASINO_ARCH = linuxpc-ifort-lam-parallel. NO!
Are you sure that everything defined in CASINO/arch/data/linuxpc-ifort-lam-parallel.arch
(and in all the subfiles it includes) are appropriate for your machine? My OS is SuseLinux 12.1 64bit and an 8core PC.

(5)Above mentioned missing lib`s are all present in the /mpi-lam/64lib directory and specified in my path:
A.:mpi-lam It's a typo
-----------------------------------------------
Unfortunately I could not upload an attachment in *.txt or *.doc. Find bellow my second trial installation sequence
In the new compilation I defined 'export linuxpc-ifort-parallel' and it is specified in .bashrc
CASINO v. 2.12.1 installation sequence. Option: automatic

./installer

Current status:
- You have the following CASINO_ARCHs defined:
- linuxpc-ifort [fully compiled]
- linuxpc-gcc [fully compiled]
- linuxpc-ifort-lam-parallel [not fully compiled] [current]

Choose an option:
[c] Compile CASINO for already-configured CASINO_ARCHs
[s] Sort/remove configured CASINO_ARCHs
[a] Auto-detect valid CASINO_ARCHs for this machine
[p] Pick a specific CASINO_ARCH for this machine
[n] Create a new CASINO_ARCH for this machine interactively
[y] Install CASINO syntax highlighting for various text editors
Install required software using package manager (requires root access)
[r] Restore the CASINO distribution directory to its original state
[q] Save (unmodified) configuration and quit the installer
[x] Quit the installer
CHOICE> a

Found the following matching CASINO_ARCHs:
[1] linuxpc-absoft-parallel [generic match]
[2] linuxpc-gcc [generic match]
[3] linuxpc-ifort [generic match]
[4] linuxpc-ifort-lam-parallel [generic match] [current]
[5] linuxpc-ifort-lam-parallel.saratoga [generic match]
[6] linuxpc-ifort-lsf-parallel [generic match]
[7] linuxpc-ifort-parallel [generic match]
[8] linuxpc-ifort-pbs-parallel [generic match]
[9] linuxpc-ifort-pbs-parallel.teragrid [generic match]
[10] linuxpc-ifort-pbs-parallel.wei238 [generic match]


Enter the number of the CASINO_ARCH you would like to enable on this machine.
You can enter multiple numbers separated with spaces. Type 'info' followed by
one or more numbers to display additional information about each CASINO_ARCH.
Leave empty to skip.
CHOICE> 2 3 7

Current status:
- You have the following CASINO_ARCHs defined:
- linuxpc-ifort [fully compiled]
- linuxpc-gcc [fully compiled]
- linuxpc-ifort-lam-parallel [not fully compiled] [current] (See remark * bellow)
- linuxpc-ifort-parallel [fully compiled]

Choose an option:
[c] Compile CASINO for already-configured CASINO_ARCHs
[s] Sort/remove configured CASINO_ARCHs
[a] Auto-detect valid CASINO_ARCHs for this machine
[p] Pick a specific CASINO_ARCH for this machine
[n] Create a new CASINO_ARCH for this machine interactively
[y] Install CASINO syntax highlighting for various text editors
Install required software using package manager (requires root access)
[r] Restore the CASINO distribution directory to its original state
[q] Save configuration and quit the installer
[x] Quit the installer without saving
CHOICE> c

The following CASINO_ARCHs are configured (it is possible that not all of them
can be compiled from this machine depending on your set-up):

[1] linuxpc-ifort
[2] linuxpc-gcc
[3] linuxpc-ifort-lam-parallel
[4] linuxpc-ifort-parallel

At the prompt below enter the numbers corresponding to the CASINO_ARCHs you
would like to compile, separated by spaces.

You can specify which optional compile-time features to enable by appending
':<feature>' to each number. Available <features> include:
- 'Openmp' for building OpenMP support
- 'Shm' for building the SMP shared-memory blips facility
- 'OpenmpShm' for building a version with both features enabled

Enter what to compile (e.g., '1 1:Shm 2 3:Openmp 2:OpenmpShm'), or leave empty
to go back to main menu without compiling anything:
CHOICE> 1 2 4


compilation of
COMPILING CASINO FOR linuxpc-ifort
COMPILING CASINO FOR linuxpc-gcc
COMPILING CASINO FOR linuxpc-ifort-parallel


did not show compiling errors

**************************
Test error using 'runqmc'

bcramer@linux-1bj8:~/CASINO/examples/atom/argon> runqmc
WARNING: Binary directory
/home/bcramer/CASINO/bin_qmc/linuxpc-ifort-lam-parallel not found.

ERROR: Quitting.
*************************
*Remark

• Also by using `gaussiantoqmc` to covert the file I receive de message `Wrapper failed to find gaussiantoqmc for CASINO_ARCH=linux-pcifort-lam-parallel`

It seems that my problem is related to the compilation procedure.

In my first installation I tried to compile with `linux-pcifort-lam-parallel` also specifying it in my .bashrc but the errors are those listed in my first e-mail and also followed by
linuxpc-ifort-lam-parallel [not fully compiled] [current] which seems to be my compiling problem.
----------------------------------

Regards
Bruno
Mike Towler
Posts: 239
Joined: Thu May 30, 2013 11:03 pm
Location: Florence
Contact:

Re: gaussiantoqmc test

Post by Mike Towler »

Hi Bruno,

OK - a few minor things first.
In the new compilation I defined 'export linuxpc-ifort-parallel' and it is specified in .bashrc
CASINO v. 2.12.1 installation sequence.
Be careful with these typos - I get stressed. Presumably you mean export CASINO_ARCH='linuxpc-ifort-parallel' ?

And yet all your questions refer to the case when CASINO_ARCH=linuxpc-ifort-lam-parallel .Why are you therefore setting CASINO_ARCH=linuxpc-ifort-parallel?

In any case you shouldn't try to do this yourself. When you use the [q] command of the install script ('Save configuration and quit') this is exactly what the install script does i.e. it will write a '.bashrc.casino' file which is automatically sourced from your .bashrc, whence all your environment variables and path etc. are defined (You will need to either 'source ~/.bashrc' or logout and login again for the changes to take effect). You also seem to be trying to define four different CASINO_ARCHs.. the stuff in .bashrc.casino will allow you to switch between them through the 'casinoarch' command that it defines.

Also - I'm not sure why you're trying to define so many CASINO_ARCHs. This is only normally necessary in order to use different compilers. Why are you defining e.g. linux-ifort, linuxpc-ifort-parallel, AND linuxpc-ifort-lam-parallel? Either the machine has more than one processor, or it doesn't. Either there is a batch queue system (LAM in this case), or there isn't. You say your machine is 'SuseLinux 12.1 64bit and an 8core PC' - this sounds like your own personal machine which almost certainly doesn't need to use LAM, so I would say you just want to define linuxpc-ifort-parallel (and maybe linuxpc-gcc-parallel if you have the GNU compiler installed and you want to try an alternative compiler). Let's just try one first and stick with it, OK?

So:

Question 1: Is your machine correctly set up so that it's Fortran compiler and Openmpi library can be used to compile a generic 'hello world' program (not CASINO) which works in parallel? (through some kind of wrapper like mpif90).

Question 2: If you type 'echo $CASINO_ARCH on your command line' what does it tell you? (at the moment you're having your gaussiantoqmc problem). [I repeat, gaussiantoqmc is a red herring - it's just telling you your compiler is not set up correctly for your chosen CASINO_ARCH.]

Question 3: Why exactly are you trying to set up linuxpc-ifort-lam-parallel on your machine. Is it because the Automatic option of the install script tells you to, or do you have some deeper reason? If you do have a deeper reason, why are you using LAM on an 8-core personal PC?

Question 4: Is it possible that you're taking the output of the 'Automatic' option of the install script too seriously? It hasn't found an exact match (i.e. no-one has set up CASINO on your machine before) so it's suggesting a whole bunch of generic matches which could in principle be set up on your machine (but which might not actually work). I think you would do better choosing option [n] 'Create a new CASINO_ARCH for this machine interactively' where the script will ask you questions about the name of the compiler, the locations of your libraries, and so on. What happens if you try that?

I'm sorry if this all seems a bit complicated. I mean the Android or Iphone app that you download on your phone works out of the box because they know exactly what kind of machine you're tring to install it on. CASINO supposedly supports every kind of computer ever invented, so despite the implications of the word 'Automatic' some kind of intelligent user input is often required.

Cheers,
Mike
Bruno_Cramer
Posts: 4
Joined: Sun Dec 22, 2013 3:48 pm

Re: gaussiantoqmc test

Post by Bruno_Cramer »

Dear Mike,

I used your recommendation

"...choosing option [n] 'Create a new CASINO_ARCH for this machine interactively' ..." and this solved the install problem. I also changed to the CASINO beta version.
I tested 'runqmc' with some of the CASINO examples and it worked fine. Also the conversion of the Gaussian file c2h2 with 'gaussiantoqmc' was ok and the files were tested with 'runqmc' without problems.
Based on the User's Guide I will take a deeper look at the program capabilities and try to get acquainted with it.
Thank you
Regards
Bruno
Mike Towler
Posts: 239
Joined: Thu May 30, 2013 11:03 pm
Location: Florence
Contact:

Re: gaussiantoqmc test

Post by Mike Towler »

Cool. Have fun!

M.
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