2.4 Set up your environment
You will need to define a couple of environment variables, preferably in your login script.
If you are using a of batch system, such as PBS, SGE or LSF, then make sure that the variables are set not only for interactive work but also for batch use. In a distributed parallel environment, like a Linux cluster, make sure that these environment variables are set on all nodes.
The most important environment variables are automatically passed on from the master process to the child processes in case of a parallel run. Thus the values set on the node where you start the program will override any value you may have set on the nodes where the child processes are running. Typically, you should still set the environment variables on all nodes since you won't know in advance on which node the master will run.
Hint: set the SCM_DEBUG environment variable to "yes" before running ADF to see values of relevant environment variables for each process. This may be especially useful if you suspect that some variables are not propagated through mpirun command to the master node.
The following environment varables must always be set for all ADF versions.
| Name | Possible value | Description |
| ADFHOME | $HOME/adf2008.01 | full path of the ADF installation directory (see section 2.3) |
| ADFBIN | $ADFHOME/bin | full path ADF directory for scripts and binaries |
| ADFRESOURCES | $ADFHOME/atomicdata | full path of the directory with the ADF database (basis sets and so on) |
| SCMLICENSE | $ADFHOME/license.txt | full path to the license file |
The following environment variables may be required for any parallel (MPI or PVM) version.
| Name | Possible value | Description |
| NSCM | 16 | default number of parallel processes; do not put it in the shells's rc file but rather set this variable per job |
| SCM_TMPDIR | /scratch/$USER | full path of the directory where all processes will create their temporary files. See also sections 2.8 and 4. |
The following environment variables are relevant for MPI versions only.
| Name | Possible value | Description |
| SCM_MACHINEFILE | $HOME/.machine | full path-name of the file containing a list nodes to use; it should only be set if multiple computers are used without a batch system. |
The following environment variables are relevant for a PVM version only.
| Name | Possible value | Description |
| PVM_ROOT | $HOME/pvm3 | full path of the main PVM installation directory |
| PVM_ARCH | SGI6 | architecture code for your machine (NOTE: use SGI6 on SGI IRIX) |
| SCMSPAWNSCRIPT | $ADFBIN/adfs | full path of the script used by the PVM daemon to start slave nodes |
The following environment variables are relevant for the GUI modules
| Name | Default Value | Description |
| SCM_ERROR_MAIL | no error e-mail sent | e-mail address for error reports |
| SCM_GUIRC | $HOME/.scm_guirc | location of the preferences file |
| SCM_TPLDIR | none (no extra templates loaded) | location of the templates directory |
| SCM_STRUCTURES | none (no extra structures loaded) | location of the structures directory |
| SCM_RESULTDIR | none (current directory used) | location of the results directory |
| DISPLAY | required (for all X11 programs) except on Windows | X-window display to use |
| SCM_MOPAC | none (default script $ADFBIN/mopac.scm will be used) | command to start MOPAC |
| SCM_QUEUES | none (ADFjobs will search the remote $HOME/.scmgui) | path to the dynamic queues directory |
The following environment variables are relevant for source distributions only, and only at the configure time.
| Name | Possible value | Description |
| MPIDIR | /opt/hpmpi | full path of the directory where MPI library is installed. This variable is required at configure time when a non-standard MPI library is used. Important: Do not set MPIDIR when building an HP-MPI or OpenMPI version of ADF with MPI libraries delivered with ADF. |
| MATHDIR | /opt/intel/mkl/10.0.011 | (optional) installation directory of the Intel MKL library |
The following environment variables may be set to modify other aspects of ADF execution. All of them are optional and some are used for debugging only.
| Name | Possible value | Description |
| SCM_IOBUFFERSIZE | 64 | Size of memory buffer for scratch files, in megabytes. See also section 4. |
| SCM_VECTORLENGTH | 128 | Block length used in the numerical integration routines. See also section 4 |
| SCM_RCV_TIMEOUT | 900 | (PVM only) time (seconds) to wait for messages |
| SCM_MAX_RCV_TIMEOUTS | 2 | (PVM only) maximum number of timeouts |
| SCM_ALARMTIME | 1800 | Time (seconds) to wait for messages using ALARM signal, 0 disables timeouts. Currently the default setting is zero, because this feature may not work on some platforms. |
| SCMBCOP | 1 | Broadcast algorithm (not to be changed for MPI versions) |
| SCMGAOP | 5 | Gather algorithm (not to be changed for MPI versions) |
| SCMCBOP | 1 | Combine alogrithm (not to be changed for MPI versions) |
| SCM_DEBUG | yes | Set to debug SCM_TMPDIR usage and environment variables (also see above) |
| SCM_NOMEMCHECK | yes | Disable memory checks |
| SCM_NODOMAINCHECK | yes | Disable domain check for license |
| SCM_TRACETIMER | yes | For debugging only: produce additional output on ADF internal timer entry/exit |
| SCM_DEBUG_ALL | yes | For debugging only: equivalent to specifying DEBUG $ALL in the input |
