AMPAC 8 with Graphical User Interface Release Notes - Compaq Tru64 Unix Version ----------------------------------------- Copyright (c) 1996-2005 Semichem, Inc. All Rights Reserved. All compilations were done using Digital UNIX V5.1B (Rev. 2650) [OSFBASE540]. You 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. System Information ------------------ To determine your OS level, use the following command: /usr/bin/uname -a Additional OS information may be found using: cat /etc/motd To determine which packages are installed, use the following command: /usr/sbin/setld -i | more CXML Math Libraries -------------- AMPAC uses CXML math libraries provided by HP. This library contains high-performance math routines optimized for use with Tru64 machines. These libraries are now included with distribution of AMPAC. There is no need to separately install CXML. (If you do wish to install CXML anyways, follow the instruction below for "installing CXML". In some cases, you may need to configure how AMPAC uses CXML. To do that, follow the "Configuring CXML" instructions below. AMPAC now uses the parallel version of the CXML library. Computers with multiple processors will now be able to take advantage of the processors during the math routines and so should see a significant improvement in performance. For computers with a single processor, there is no benefit or penalty (relative to the serial version of the CXML library). For multi-processor machines, the environmental variable OMP_NUM_THREADS should be set appropriately to get the benefit of multiple processors. Note: OMP_NUM_THREADS should never be set higher than the actual number of processors or there will be a significant performance penalty. GL Libraries ------------ The GUI will only run using OpenGL. You will need to install the Open3D package: OSFOPENGL540 installed OpenGL Runtime (Windowing Environment) OSFOPENGLDEV540 installed OpenGL Software Development (Windowing Environment) See "Troubleshooting" section for more details on OpenGL. ============================= Installing Compaq Fortran RTL ============================= Up to date run time libraries (RTL) are required and can be downloaded from the Compaq website. html://www.compaq.com/fortran/downloads.html Under "HP Fortran for Tru64 Unix" select the "Latest run-time library subset (DFARTLnnn, where nnn>=406)" and save it to your computer. Untar the downloaded file and "cd" to the directory with the untar'ed contents. You must have root permission to install, so "su root" if necessary. Call setld to start the installation ("/usr/sbin/setld -l ."). Select the RTL subset to install (DFARTL###). The installer should be able to determine the configuration of your system (Ev4, Ev5, or Ev6) and install the most optimal version. Once done, confirm that everything has been properly installed. Using setld, you should get something like this /usr/sbin/setld -i | grep -i dfartl DFARTL406 installed Compaq Fortran RTL #406 for Compaq Tru64 UNIX Alpha Systems (f90 and f77) ========================== Installing CXML (optional) ========================== The CXML math libraries are now shipped directly with AMPAC, so there is no need to separately install these libraries. However, if CXML libraries are required for other applications or if a newer CXML library becomes available, the user may choose to install them. In that case, follow the installation instructions below and then reconfigure AMPAC to use the system's CXML libraries. (See Configuring CXML below.) To install CXML, you must have root access, Tru64 Unix version 5.1B or later, and up-to-date Fortran Run Time Libraries (DFARTLnnn, where nnn>=406). Make sure that the system libraries and Fortran Run Time Libraries are up-to-date before installing. The CXML home page is: html://www.compaq.com/math Detailed installation instructions can be found under "documentation" and the library itself can be found under "download." Select "download" and follow the instructions. Choose the CXML library appropriate for your system (three choices are Ev4, Ev5, and Ev6). Untar the package to a temporary directory. Next, "cd" to the directory containing the untar'ed contents. Call setld to start the installation ("/usr/sbin/setld -l ."). During the installation, several options must be chosen: 1) A choice of 5 subsets to install are presented. Select the appropriate libraries. Subsets XMDCOM ("common files") and XMDLIBj (j=4, 5, or 6, "CXML libraries") are necessary subsets XMDHTM and XMDMAN are documentation libraries and are optional subset SCIPORT ("Cray compatibility library") is unnecessary. 2) A choice of serial, parallel, or both. Parallel is needed only if more than one CPU is present. 3) A choice of archive (*.a library), shared (*.so library), or both. The shared library is required. 4) Confirm placing symbolic link to libraries in the standard library. Accept this. Once done, confirm that everything has been properly installed. Using setld, you should get something like this /usr/sbin/setld -i | grep -i cxml XMDCOM520 installed CXML Common Files for the Extended Math Lib, V5.20 XMDHTM520 installed CXML Reference (man)Pages in HTML format XMDLIB6520 installed CXML Extended Math Libraries (Serial and Parallel) for Ev6, V5.20 XMDMAN520 installed CXML Reference (man)Pages XMDSCI520 installed CXML V5.20 SCIPORT library Note, that XMDHTM and XMDMAN are both optional reference material and will only appear if they were installed. Likewise, XDMSCI will only appear if it was installed. ================ Configuring CXML ================ The CXML math libraries comes in several versions each of which is optimally tuned to a specific family of processors. Currently the CXML library exists in separate versions for EV4, EV5, and EV6 processor families. CXML does not currently exist for EV7 or later processors; however, the CXML EV6 library will run efficiently on these machines. By default, the choice of CXML library is configured during installation. The user may reconfigure this at any time. To do this: cd $AMPAC_DIR ./config_ampac.csh {cxml_option} If no "cxml_option" flag is specified, "config_ampac.csh" will use "/usr/sbin/sizer -implver" to determine the processor family on that machine and choose the corresponding CXML library. So, if "sizer" identifies the processor as "EV6", it will configure for the CXML library tuned for EV6 processors. However, you can specify which CXML version you wish to use by using the appropriate "cxml_option" flag. Use "-ev4", "-ev5", "-ev6", or "-ev7" to correspond to processor families EV4, EV5, EV6, and EV7 respectively. (Note: "-ev7" will give a warning message and then configure for EV6, since there are currently no EV7 CXML libraries.) So, if you want the CXML libraries for EV6 processors, you would enter: ./config_ampac.csh -ev6 There is an additional configuration option to use, if you do not want to use the CXML libraries packaged with AMPAC. This option is useful if you have a newer version of the CXML library than is distributed with AMPAC. To use the CXML libraries installed on the system, use the "-system_cxml" flag. ./config_ampac.csh -system_cxml Do not use this configuration option unless CXML is installed on your system or else AMPAC may fail to run! =============== Troubleshooting =============== 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 (CXML or Fortran Run Time Libraries) ------------------------------------------------------ If AMPAC reports a missing, the two most common causes are missing CXML math libraries or out-of-date Fortran Run Time Libraries. For these two cases, follow the instructions here and for all other missing libraries, see the "Missing Libraries" section below. If the "check_env.csh" test script or running AMPAC indicates that AMPAC is missing "libcxmlp.so" then the CXML library is the source of the problem. AMPAC now comes with CXML libraries, so this problem should not occur unless AMPAC has been configured with the "-system_cxml" option and CXML is not currently installed on that system. Either configure AMPAC to use the CXML libraries that come with it (see "Configuring CXML" above) or correctly install the CXML libraries (see "installing CXML" above). The Compaq Fortran Run Time Libraries (RTL) need to be up to date and include library (libm_c32.so). If this is not the case, then follow the instructions "Installing Compaq RTL" above. 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". GUI reports missing Libraries ---------------------------- Symptom: The AGUI application fails to launch and reports that libraries are missing. The AGUI program requires the Open3D OpenGL libraries. These libraries may not be installed on systems that do not have a 3D capable graphics card installed. If you do not have a 3D capable graphics card, we recommend that you contact your Digital Representative about purchasing one. Once the Open3D is installed, verify that all the necessary components have been properly installed. Here is an example of a typical Open3D installation as reported by setld: /usr/sbin/setld -i | grep -i opengl /usr/sbin/setld -i | grep -i opengl 3X0GLBASE515 not installed PowerStorm 3x0 v1.5.1 for V5.0 OpenGL 3X0GLBASE523 not installed PowerStorm 3x0 v2.2 for V5.1A OpenGL 3X0GLBASE524 installed PowerStorm 3x0 v2.3 for V5.1A or V5.1B OpenGL OSFOPENGL540 installed OpenGL Runtime (Windowing Environment) OSFOPENGLDEV540 installed OpenGL Software Development (Windowing Environment) The first three entries are Hardware Drivers for specific graphics cards. Note, you must be sure that the OpenGL subsets are installed for the AGUI application to launch. System Thrashes --------------- Symptom: All processes slow and the system response becomes sluggish. This usually indicates your system is running low on physical memory. I received the following suggestion from Compaq. It seems to help ease this problem. However, the obvious solution is to avoid loading your system with too many jobs. --- Add the following 2 lines to the end of /etc/syconfigtab --- vm: vm-page-free-optimal=1 ----- You must reboot for this to take affect.