AMPAC 8 with Graphical User Interface Release Notes - Silicon Graphics Version ---------------------------------------- Copyright (c) 1996-2005 Semichem, Inc. All Rights Reserved. All compilations were done using the IRIX64 6.5.22m OS. Testing has also been performed on IRIX 6.5. You will need this level of system software to support AMPAC. If you are running an older version of the system software, we suggest you update to ensure proper compatibility. Newer versions will support the version compiled under IRIX64 6.5. For operating system upgrades, contact SGI or visit their suportfolio website at: http://support.sgi.com/surfzone System Information ------------------ To determine your OS level, use the following command: uname -a The output should look something like: IRIX64 caleb 6.5 10070055 IP35 More detailed information about the operating system can be found with: sysconf To access information about processor type, available memory, or other hardware specific information use: hinv SGI Fortran Runtime Libraries ----------------------------- AMPAC requires some runtime libraries (e.g., libfortran.so) which come from the packages ftn_eoe.sw.lib and ftn_eoe.sw64.lib. These packages should be in the standard IRIX 6.5 software distribution need to be installed before using AMPAC. SGI SCSL Math Library --------------------- AMPAC uses the SCSL library provided by SGI. This library contains high-performance math routines optimized for use with SGI machines. More information on SCSL and how to download it can be found at: http://www.sgi.com/software/scsl.html AMPAC for Older Systems ----------------------- Semichem is officially releasing and supporting AMPAC compiled to run on MIPS4 computers (R5000, R8000, R10000, and later processors). If a MIPS2 or MIPS3 version of AMPAC is desired contact Semichem Customer Support for availability. (MIPS2 and MIPS3 can run on R4000 or later processors.) Semichem cannot officially support these older versions or guarantee full functionality. 32-bit Verses 64-bit Executables -------------------------------- AMPAC is available in both 32-bit and 64-bit executable versions. The 32-bit version requires less memory than the 64-bit version for an equivalent job. However, 32-bit executables place a limitation on addressable space that can prevent very large jobs from running. The exact limitation depends on the specific job but some general guidelines can be given. For a simple optimization with no C.I., the 32-bit limitation is around 1,000 atoms. For small molecules, 32-bit addressing limits C.I. to around 5,000 microstates. SGI distribution of AMPAC contains both the 32-bit and 64-bit versions of the key executables. By default, AMPAC is set to use 64-bit executables but this can be changed by using the "config_ampac.csh" script in the main AMPAC directory. Calling "config_ampac.csh" without arguments, will cause the script to an option according the operating system. Adding "-64" will force the script to specify 64-bit versions and "-n32" will force the 32-bit versions. For those running IRIX (rather than IRIX64), you will need to run "config_ampac.csh" to force the use of 32-bit executables. =============== Troubleshooting =============== Cannot execute binary file -------------------------- The older IRIX only supports 32-bit versions of AMPAC, while the newer IRIX64 systems supports both 64-bit and 32-bit versions of AMPAC. (See discussion above.) By default, AMPAC is configured to run using 64-bit executables, which is appropriate for most modern systems. For IRIX, however, this causes an immediate failure because 64-bit libraries will not be available. To fix this problem, AMPAC must be configured to run 32-bit executables. To do this: cd $AMPAC_DIR ./config_ampac.csh -n32 Note: this may require administrator privileges. To check which set of executables is currently enabled: ls -l $AMPAC_DIR/program/ampac.exe If the soft link points to "ampac_64.exe" then it is configured for 64-bit and if it points to "ampac_n32.exe" it is configured for 32-bit. AMPAC Fails Silently -------------------- Symptom: Nothing happens when AMPAC is called but no error messages appear. If AMPAC or one its utilities fail silently, this may indicate a system library incompatibility problem. By default, _RLD_ARGS is set to suppress run-time warnings and error messages. Clearing this environmental variable will allow any diagnostic error messages to appear. To do this use: unsetenv _RLD_ARGS (for csh or tcsh shells) -or- unset _RLD_ARGS (for sh, ksh, or bash shells) After changing _RLD_ARGS, rerun AMPAC. Examine any messages that are produced when AMPAC is run. If the output indicates a missing library, then skip down to section on "Missing Libraries." For other error messages, contact Semichem Customer Support for help and include this output along with a description of the problem. Missing Libraries ----------------- AMPAC relies on libraries that must be loaded at run time. In the event that AMPAC is unable to find all of its required libraries, then it will print out an error message and exit. A diagnostic script, "check_env.csh", has been provided to identify and resolve the most common problems. Instructions on how to use this diagnostic can be found in README.txt. If that fails to resolve the problem, follow the procedure given here. 1) The user must be in or switch to either a csh or tcsh shell. If the user is already running in csh or tcsh, then nothing needs to be done. For users running sh, ksh, or bash shells, issue the following command: /usr/bin/csh (or /usr/bin/tcsh) (If you are unsure of which shell you are using, issue the command "echo $0" to identify it.) AMPAC can run in any of the common shell environments, however, the scripts that run AMPAC are csh based and so this diagnostic procedure requires a csh environment. 2) Initialize AMPAC information. To do this: cd {main AMPAC directory} source init_ampac.csh If AMPAC_DIR has already been properly set, then this step may be skipped. 3) Manually initialize AMPAC's run time environment. This must been done first to insure that the proper environmental variables are being tested. source $(AMPAC_DIR)/bin/ld_env.csh Normally, this is done automatically by the scripts that run AMPAC. It is done this way, so that only the processes that are actually used to run AMPAC will have their environmental variables altered and so these changes disappear once the job is finished. This prevents AMPAC's changes to environmental variables from interfering with other processes. For this diagnostic procedure, we need set the same environment used by the AMPAC scripts. (Note, "ld_env.sh" also exists but is not used by AMPAC, even if AMPAC is being used from a sh-based shell. That script is provided only for completeness.) 4) Check the library dependencies. Use: cd $(AMPAC_DIR)/program ldd ampac.exe The output from "ldd" lists each of the libraries required to run AMPAC. Note any libraries that have not been found by the system. If the required library has been found, the exact location of the library that will be loaded in at run time is given. Since more than one version of a given library may exist on the system, verify that the correct library is being used. 5) Verify that the missing library exists on your system. Use: find / -name "missing library" -print If the library is not found, then it must be installed before AMPAC can be used. Consult your system administrator or the system documentation. If the library is found, note the directory in which it is located. 6) Edit the script "$(AMPAC_DIR)/bin/ld_env.csh" and insert library directory into each of the link library search path variables. Run AMPAC to verify that the problem has been resolved. If there are additional missing libraries, go back to step 3. 7) If a shell was started for this diagnostic test (step 1), then exit it. This can be done by typing ctrl-D or "exit". Configuring Swap Space ---------------------- AMPAC needs large blocks of memory an/or disk space to run effectively, especially for bigger versions of the program used for larger molecules and extensive CI. This executable image space comes from both hard disk and physical memory. The hard disk space set aside for memory use is referred to as swap space and the user must usually configure this on each system for use of AMPAC. When configured in the default arrangement, the system has only 40MB of swap space allocated, and this is simply not enough. Following are two procedures for allocating swap space. (Note that the swap space defined by either of the two following procedures will be immediately subtracted from the available space on your hard disk.) We therefore recommend that you create a swap file for use with AMPAC using the following procedures. CAREFULLY READ THE UNIX MAN PAGES ON SWAP BEFORE IMPLEMENTING IT. You can examine the present swap settings on your machine by using the Unix command: swap -ln ************************************************************* Procedure 1: Temporary Swap Space 1. Login as root. 2. Create a subdirectory: mkdir /swap 3. Create a swap file using the command: /usr/sbin/mkfile XXXm /swap/swap1 where XXX is the size of the swap file in MB. This sequence of commands will create the swap file and keep it active until the next system boot. 4. Add the swap file resource: /sbin/swap -a /swap/swap1 ************************************************************* Procedure 2: Permanent Swap Space 1. Complete "Procedure 1" above. 2. Edit the file /etc/fstab and add the following line: /swap/swap1 swap swap pri=3 0 0 This will re-create the swap file at each new boot of the system.