MOLCAS manual:
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Subsections
MOLCAS, as shipped, is configured with some default settings. You can change
some of these easily.
You can change default settings used in MOLCAS (like memory usage, default
scratch area, policy in saving files, etc.)
by editing MOLCAS resource file: global resource file $MOLCAS/molcasrc or
user resource file $HOME/.Molcas/molcasrc.
3.1.1 Dynamic memory
Most modules in MOLCAS utilize dynamic memory allocation. The amount of
memory each module allocate is controlled by the environment variable
MOLCAS_MEM. The amount of memory allocated is
- MOLCAS_MEM is undefined — 2048Mb of memory is allocated
- MOLCAS_MEM=nn — nnMb is allocated.
If this amount cannot be allocated, the module stops.
3.1.2 Disk usage
Today many workstations utilize 64-bit integers
and addressing. However, old UNIX workstations and PC's had 32-bit integers
resulting in a file size limit of 2GB.
To circumvent these limitations, the I/O routines
of MOLCAS support multifile files, where a ``file'' is in reality a
logical file consisting of several physical files. The size limit of
these physical files is controlled by the environment variable
MOLCAS_DISK. The use of MOLCAS_DISK is not recommended.
MOLCAS is shipped with a number of default setup files located
in directory cfg/. The defaults in these files are set to
a fairly safe level, but not necessary optimal. What you can change
to improve performance is
- Compiler flags
- Mathematical (blas) libraries
The simplest way to set up optimization level, and/or compile MOLCAS with various BLAS libraries is to use configure -setup. This
interactive script helps to make a proper selection of flags for
improvement of MOLCAS performance.
If you do decide to try to improve the performance we recommend that you
create a new setup file, for example, cfg/local.cfg and
modify this file. It is not unlikely that your attempts to optimize
the codes will lead you to a case where some modules work and others do not.
In such a scenario it can be fruitful to have two copies of
MOLCAS, one ``safe'' where all modules work and one ``fast'' where
some modules do not function properly.
Changing the compiler flags is the easiest. Using the most
aggressive optimization flags do sometimes lead to problems for
some of the modules. We have tried to choose an optimization level
that yields functioning code, but still reasonable fast.
For some systems there is a predefined set of compiler flags for
aggressive optimization. To compile MOLCAS with these flags you
should run configure with flag -speed fast.
Note that this aggressive optimization level is not supported
by the MOLCAS team. In other words, you are using it at your own
risk.
For some platforms you can utilize the vendor blas libraries. This
will certainly yield better performance, but may not work on all
platforms.
During configuration of MOLCAS it is possible to specify
an external BLAS/LAPACK library. Use a flag -blas TYPE
to specify the type of BLAS libary: lapack (for a standard lapack
library), Goto (for GotoBLAS), Atlas (for ATLAS), MKL (for Intel MKL).
You should also specify a flag
-blas_lib -Wl,--start-group -L/path/to/blas -lmy-blas -Wl,--end-group
specifying the link options.
For example, to configure MOLCAS with Intel MKL library,
you should issue a command ./configure -compiler intel -blas MKL
-blas_lib -Wl,--start-group /opt/intel/mkl/lib/intel64 -lmkl_gf_ilp64 -lmkl_sequential
-lmkl_core -Wl,--end-group
To compile MOLCAS with CUDA BLAS library, first, you have to compile
the fortran wrapper provided by nVIDIA:
CUDA=/path/to/cuda/
FLAGS=-m64
gcc $FLAGS -I$CUDA/include/ -I$CUDA/src/ -c $CUDA/src/fortran_thunking.c -o \
$MOLCAS/lib/fortran.o
./configure -blas CUDA -blas_dir $CUDA/lib
or, if on a 64bit system:
./configure -blas CUDA -blas_dir $CUDA/lib64
After making changes to the setup files you have to issue the commands
make veryclean, ./configure and make in the MOLCAS root
directory. It is highly recommended to run the verification suite after
any changes in configuration file.
3.1.4 Customizing handling of files
The location and attributes of files used by MOLCAS are defined in PRGM files.
The master copy of these files is located at the data directory in the MOLCAS root.
A user can copy these files and modify them. The highest priority is given
to the files located in the subdirectory prgm in the current (CurrDir) directory,
next the $HOME/.Molcas and finally the original location at $MOLCAS/data.
The simplest way to manipulate prgm files is to use the molcas prgm command.
A command molcas prgm init global makes a copy of the prgm files in the .Molcas
directory. molcas prgm init local creates a prgm subdirectory, and copies the prgm files
into it.
The editing of the files can be performed by your favourite editor, or by the molcas prgm script.
The structure of PRGM files is simple. The field (file) is followed by the
FORTRAN name (as this file is known for MOLCAS), real file name (as this file is known by the Operating system), and finally the attributes.
The attributes are listed here:
| ro |
the file is accessed for reading |
| rw |
the file is accessed for reading and writing |
| s |
the file will be saved (copied) from the scratch area |
| m |
the file will be saved (moved) from the scratch area |
| g |
the file can be visualized by program "gv/luscus" |
| t |
the file is an ASCII text |
| * |
multifile |
| . |
multifile (for internal use) |
| l |
use lustre filesystem in parallel run |
| p |
the file will be deleted |
| e |
the file will be placed to memory (see FiM) |
| f |
use an alternative file location (FastDir) |
A command molcas prgm +x ScfOrb will add the attribute `x' to all ScfOrb files. A regexp can be used for a filename.
An opposite command molcas prgm -x ScfOrb will remove the attribute `x'.
A command molcas prgm comp [global] shows the list of modifications in the local (/prgm), or global (.Molcas)
directories.
3.1.5 Improving I/O performance
In order to activate this technology for a MOLCAS scratch file, one needs to
do three things. First, please edit an external resource *.prgm (for example,
$MOLCAS/data/seward.prgm) from the $MOLCAS/data/ directory. If you don't
have access to the root MOLCAS directory, then you can simply copy the
needed resource file into your home $HOME/.Molcas/ directory and edit it there.
The editing of the file consists in adding the 'e' character to its
attributes:
original: (file) ORDINT "$WorkDir/$Project."OrdInt rw*
modified: (file) ORDINT "$WorkDir/$Project."OrdInt rw*e
Second, you need to set up the MOLCAS_FIM environment variable to 1
i.e.:
export MOLCAS_FIM=1
The third and the final step is to specify the MOLCAS_MAXMEM ( MOLCAS_MEM) parameter such that the
MOLCAS_MAXMEM-MOLCAS_MEM difference (in MW) is sufficient to host an entire
file in RAM. In other words, the MOLCAS_MAXMEM-MOLCAS_MEM difference should
exceed the original filesize.
In general, not all MOLCAS files are suitable for placing in RAM. In
particular, it is a bad idea to activate FiM for RUNFILE. In order to
identify which MOLCAS's files are proper candidates for FiM, you can simply
inspect the section "II. I/O Access Patterns" from a MOLCAS's output.
All files with high ratio of I/O random Write/Read calls are good candidates for
FiM. In particular case of the SEWARD module, the ORDINT file is
a very good candidate for FiM:
II. I/O Access Patterns
- - - - - - - - - - - - - - - - - - - -
Unit Name % of random
Write/Read calls
- - - - - - - - - - - - - - - - - - - -
1 RUNFILE 28.6/ 11.5
2 ORDINT 100.0/ 24.0
3 DNSMAT 0.0/ 0.0
4 TWOHAM 0.0/ 0.0
5 GRADIENT 88.9/ 0.0
6 DNSMAX 0.0/ 0.0
7 TWOHAX 0.0/ 0.0
8 SODGRAD 85.7/ 0.0
9 SOXVEC 85.7/ 0.0
10 SODELTA 88.9/ 0.0
11 SOYVEC 88.9/ 0.0
12 ONEINT 100.0/ 53.3
- - - - - - - - - - - - - - - - - - - -
MOLCAS is shipped with source code so you can make modifications
yourself. You are, of course, responsible for the correctness of any
such modification.
If you do make changes/additions to the source code that you feel is of
interest to other users, we encourage you to make these available.
Perhaps the best mechanism is to use the bulletin board on out homepage:
http://www.molcas.org/.
Check Molcas Programming Guide for a detailed description of development
and distribution of modified code in MOLCAS .
    
Next: III. Short Guide to MOLCAS
Up: 3. Maintaining the package
Previous: 3. Maintaining the package
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