NAMD 2.7b1 Release Notes
+--------------------------------------------------------------------+ | | | NAMD 2.7b1 Release Notes | | | +--------------------------------------------------------------------+ This file contains the following sections: - Problems? Found a bug? - Running NAMD - Compiling NAMD - Memory Usage - Improving Parallel Scaling - Endian Issues ---------------------------------------------------------------------- Problems? Found a bug? 1. Download and test the latest version of NAMD. 2. Please check NamdWiki, NAMD-L, and the rest of the NAMD web site resources at http://www.ks.uiuc.edu/Research/namd/. 3. Gather, in a single directory, all input and config files needed to reproduce your problem. 4. Run once, redirecting output to a file (if the problem occurs randomly do a short run and include additional log files showing the error). 5. Tar everything up (but not the namd2 or charmrun binaries) and compress it, e.g., "tar cf mydir.tar mydir; gzip mydir.tar" Please do not attach your files individually to your email message as this is error prone and tedious to extract. The only exception may be the log of your run showing any error messages. 6. For problems concerning compiling or using NAMD please consider subscribing to NAMD-L and posting your question there, and summarizing the resolution of your problem on NamdWiki so that others may benefit from your experience. Please avoid sending large attachments to NAMD-L by posting any related files on your web site or on BioCoRE (http://www.ks.uiuc.edu/Research/BioCoRE/, in BioFS for the NAMD public project) and including the location in your message. 7. For bug reports, mail namd@ks.uiuc.edu with: - A synopsis of the problem as the subject (not "HELP" or "URGENT"). - The NAMD version, platform and number of CPUs the problem occurs (to be very complete just copy the first 20 lines of output). - A description of the problematic behavior and any error messages. - If the problem is consistent or random. - The URL of your compressed tar file on a web server. 8. We'll get back to you with further questions or suggestions. While we try to treat all of our users equally and respond to emails in a timely manner, other demands occasionally prevent us from doing so. Please understand that we must give our highest priority to crashes or incorrect results from the most recently released NAMD binaries. ---------------------------------------------------------------------- Running NAMD NAMD runs on a variety of serial and parallel platforms. While it is trivial to launch a serial program, a parallel program depends on a platform-specific library such as MPI to launch copies of itself on other nodes and to provide access to a high performance network such as Myrinet or InfiniBand if one is available. For typical workstations (Windows, Linux, Mac OS X, or other Unix) with only ethernet networking (hopefully gigabit), NAMD uses the Charm++ native communications layer and the program charmrun to launch namd2 processes for parallel runs (either exclusively on the local machine with the ++local option or on other hosts as specified by a nodelist file). The namd2 binaries for these platforms can also be run directly (known as standalone mode) for single process runs. For workstation clusters and other massively parallel machines with special high-performance networking, NAMD uses the system-provided MPI library (with a few exceptions) and standard system tools such as mpirun are used to launch jobs. Since MPI libraries are very often incompatible between versions, you will likely need to recompile NAMD and its underlying Charm++ libraries to use these machines in parallel (the provided non-MPI binaries should still work for serial runs.) The provided charmrun program for these platforms is only a script that attempts to translate charmrun options into mpirun options, but due to the diversity of MPI libraries it often fails to work. -- Individual Windows, Linux, Mac OS X, or Other Unix Workstations -- Individual workstations use the same version of NAMD as workstation networks, but running NAMD is much easier. If your machine has only one processor core you can run the namd2 binary directly: namd2 <configfile> For multicore workstations, Windows and Mac OX X (Intel) released binaries are based on "multicore" builds of Charm++ that can run multiple threads. These multicore builds lack a network layer, so they can only be used on a single machine. The Solaris (Sparc and x86_64) released binaries are based on "smp" builds of Charm++ that can be used with multiple threads on either a single machine like a multicore build, or across a network. For best performance use one thread per processor with the +p option: namd2 +p<procs> <configfile> For other multiprocessor workstations the included charmrun program is needed to run multiple namd2 processes. The ++local option is also required to specify that only the local machine is being used: charmrun namd2 ++local +p<procs> <configfile> You may need to specify the full path to the namd2 binary. -- Linux or Other Unix Workstation Networks -- The same binaries used for individual workstations as described above (other than pure "multicore" builds and MPI builds) can be used with charmrun to run in parallel on a workstation network. The only difference is that you must provide a "nodelist" file listing the machines where namd2 processes should run, for example: group main host brutus host romeo The "group main" line defines the default machine list. Hosts brutus and romeo are the two machines on which to run the simulation. Note that charmrun may run on one of those machines, or charmrun may run on a third machine. All machines used for a simulation must be of the same type and have access to the same namd2 binary. By default, the "rsh" command ("remsh" on HPUX) is used to start namd2 on each node specified in the nodelist file. You can change this via the CONV_RSH environment variable, i.e., to use ssh instead of rsh run "setenv CONV_RSH ssh" or add it to your login or batch script. You must be able to connect to each node via rsh/ssh without typing your password; this can be accomplished via a .rhosts files in your home directory, by an /etc/hosts.equiv file installed by your sysadmin, or by a .ssh/authorized_keys file in your home directory. You should confirm that you can run "ssh hostname pwd" (or "rsh hostname pwd") without typing a password before running NAMD. Contact your local sysadmin if you have difficulty setting this up. If you are unable to use rsh or ssh, then add "setenv CONV_DAEMON" to your script and run charmd (or charmd_faceless, which produces a log file) on every node. You should now be able to try running NAMD as: charmrun namd2 +p<procs> <configfile> If this fails or just hangs, try adding the ++verbose option to see more details of the startup process. You may need to specify the full path to the namd2 binary. Charmrun will start the number of processes specified by the +p option, cycling through the hosts in the nodelist file as many times as necessary. You may list multiprocessor machines multiple times in the nodelist file, once for each processor. You may specify the nodelist file with the "++nodelist" option and the group (which defaults to "main") with the "++nodegroup" option. If you do not use "++nodelist" charmrun will first look for "nodelist" in your current directory and then ".nodelist" in your home directory. Some automounters use a temporary mount directory which is prepended to the path returned by the pwd command. To run on multiple machines you must add a "++pathfix" option to your nodelist file. For example: group main ++pathfix /tmp_mnt / host alpha1 host alpha2 There are many other options to charmrun and for the nodelist file. These are documented at in the Charm++ Installation and Usage Manual available at http://charm.cs.uiuc.edu/manuals/ and a list of available charmrun options is available by running charmrun without arguments. If your workstation cluster is controlled by a queueing system you will need build a nodelist file in your job script. For example, if your queueing system provides a $HOST_FILE environment variable: set NODES = `cat $HOST_FILE` set NODELIST = $TMPDIR/namd2.nodelist echo group main >! $NODELIST foreach node ( $nodes ) echo host $node >> $NODELIST end @ NUMPROCS = 2 * $#NODES charmrun namd2 +p$NUMPROCS ++nodelist $NODELIST <configfile> Note that $NUMPROCS is twice the number of nodes in this example. This is the case for dual-processor machines. For single-processor machines you would not multiply $#NODES by two. Note that these example scripts and the setenv command are for the csh or tcsh shells. They must be translated to work with sh or bash. -- Windows Workstation Networks --- These are no longer supported, but NAMD has been reported to compile on Windows HPC Server. -- SGI Altix -- Be sure that the MPI_DSM_DISTRIBUTE environment variable is set, then use the Linux-Itanium-MPI-Altix version of NAMD along with the system mpirun: mpirun -np <procs> <configfile> -- IBM POWER Clusters -- Run the MPI version of NAMD as you would any POE program. The options and environment variables for poe are various and arcane, so you should consult your local documentation for recommended settings. As an example, to run on Blue Horizon one would specify: poe namd2 <configfile> -nodes <procs/8> -tasks_per_node 8 ---------------------------------------------------------------------- Compiling NAMD Building a complete NAMD binary from source code requires working C and C++ compilers, Charm++/Converse, TCL, and FFTW. NAMD will compile without TCL or FFTW but certain features will be disabled. Fortunately, precompiled libraries are available from http://www.ks.uiuc.edu/Research/namd/libraries/. You may disable these options by specifying --without-tcl --without-fftw as options when you run the config script. Some files in arch may need editing to set the path to TCL and FFTW libraries correctly. As an example, here is the build sequence for 64-bit Linux workstations: Unpack NAMD and matching Charm++ source code and enter directory: tar xzf NAMD_2.7b1_Source.tar.gz cd NAMD_2.7b1_Source tar xf charm-6.1.tar cd charm-6.1 Build and test the Charm++/Converse library: ./build charm++ net-linux-x86_64 --no-shared -O -DCMK_OPTIMIZE=1 cd net-linux-x86_64/tests/charm++/megatest make pgm ./charmrun ++local +p4 ./pgm (also try running on multiple nodes) cd ../../../../.. Download and install TCL and FFTW libraries: (cd to NAMD_2.7b1_Source if you're not already there) wget http://www.ks.uiuc.edu/Research/namd/libraries/fftw-linux-x86_64.tar.gz tar xzf fftw-linux-x86_64.tar.gz mv linux-x86_64 fftw wget http://www.ks.uiuc.edu/Research/namd/libraries/tcl-linux-x86_64.tar.gz tar xzf tcl-linux-x86_64.tar.gz mv linux-x86_64 tcl Optionally edit various configuration files: (not needed if charm-6.1, fftw, and tcl are in NAMD_2.7b1_Source) vi Make.charm (set CHARMBASE to full path to charm) vi arch/Linux-x86_64.fftw (fix library name and path to files) vi arch/Linux-x86_64.tcl (fix library version and path to TCL files) Set up build directory and compile: ./config Linux-x86_64-g++ --charm-arch net-linux-x86_64 cd Linux-x86_64-g++ make (or gmake -j4, which should run faster) Quick tests using one and two processes: (this is a 66-atom simulation so don't expect any speedup) ./namd2 ./namd2 src/alanin ./charmrun ++local +p2 ./namd2 ./charmrun ++local +p2 ./namd2 src/alanin Longer test using four processes: wget http://www.ks.uiuc.edu/Research/namd/utilities/apoa1.tar.gz tar xzf apoa1.tar.gz ./charmrun ++local +p4 ./namd2 apoa1/apoa1.namd (FFT optimization will take a several seconds during the first run.) That's it. A more complete explanation of the build process follows. Note that you will need Cygwin to compile NAMD on Windows. Download and unpack fftw and tcl libraries for your platform from http://www.ks.uiuc.edu/Research/namd/libraries/. Each tar file contains a directory with the name of the platform. These libraries don't change very often, so you should find a permanent home for them. Unpack the NAMD source code and the enclosed charm-6.1.tar archive. This version of Charm++ is the same one used to build the released binaries and is more likely to work and be bug free than any other we know of. Edit Make.charm to point at .rootdir/charm-6.1 or the full path to the charm directory if you unpacked outside of the NAMD source directory. Run the config script without arguments to list the available builds, which have names like Linux-x86_64-icc. Each build or "ARCH" is of the form BASEARCH-compiler, where BASEARCH is the most generic name for a platform, like Linux-x86_64. Note that many of the options that used to require editing files can now be set with options to the config script. Running the config script without arguments lists the available options as well. Edit arch/BASEARCH.fftw and arch/BASEARCH.tcl to point to the libraries you downloaded. Find a line something like "CHARMARCH = net-linux-x86_64-iccstatic" in arch/ARCH.arch to tell what Charm++ platform you need to build. The CHARMARCH name is of the format comm-OS-cpu-options-compiler. It is important that Charm++ and NAMD be built with the same C++ compiler. To change the CHARMARCH, just edit the .arch file or use the --charm-arch config option. Enter the charm directory and run the build script without options to see a list of available platforms. Only the comm-OS-cpu part will be listed. Any options or compiler tags are listed separately and must be separated by spaces on the build command line. Run the build command for your platform as: ./build charm++ comm-OS-cpu options compiler --no-shared -O -DCMK_OPTIMIZE=1 For this specific example: ./build charm++ net-linux tcp icc --no-shared -O -DCMK_OPTIMIZE=1 The README distributed with Charm++ contains a complete explanation. You only actually need the bin, include, and lib subdirectories, so you can copy those elsewhere and delete the whole charm directory, but don't forget to edit Make.charm if you do this. If you are building a non-smp, non-tcp version of net-linux with the Intel icc compiler you will need to disable optimization for some files to avoid crashes in the communication interrupt handler. The smp and tcp builds use polling instead of interrupts and therefore are not affected. Adding +netpoll to the namd2 command line also avoids the bug, but this option reduces performance in many cases. These commands recompile the necessary files without optmization: cd charm/net-linux-icc /bin/rm tmp/sockRoutines.o /bin/rm lib/libconv-cplus-* ( cd tmp; make charm++ OPTS="-O0 -DCMK_OPTIMIZE=1" ) If you're building an MPI version you will probably need to edit compiler flags or commands in the Charm++ src/arch directory. The file charm/src/arch/mpi-linux/conv-mach.sh contains the definitions that select the mpiCC compiler for mpi-linux, while other compiler choices are defined by files in charm/src/arch/common/. If you want to run NAMD on Myrinet one option is to build a Myrinet GM library network version by specifying the "gm" option as in: ./build charm++ net-linux gm icc --no-shared -O -DCMK_OPTIMIZE=1 You would then change "net-linux-icc" to "net-linux-gm-icc" in your namd2/arch/Linux-x86-icc.arch file (or create a new .arch file). Alternatively you could use a Myrinet-aware MPI library. If you want to use MPICH-GM you must use the "gm" option, as in "mpi-linux gm icc" or equivalently you can edit charm/arch/mpi-linux/conv-mach.h to set "#define CMK_MALLOC_USE_OS_BUILTIN 1" and the other malloc defines to 0; alternately you could disable memory registration by specifying "--with-device=ch_gm:-disable-registration" when configuring MPICH-GM (at least according to the Myrinet FAQ at www.myri.com). There is a similar "ibverbs" option for InfiniBand networks, as well as an "mx" option for newer Myrinet networks. Both help performance. Run make in charm/CHARMARCH/tests/charm++/megatest/ and run the resulting binary "pgm" as you would run NAMD on your platform. You should try running on several processors if possible. For example: cd net-linux-tcp-icc/tests/charm++/megatest/ make pgm ./charmrun +p16 ./pgm If any of the tests fail then you will probably have problems with NAMD as well. You can continue and try building NAMD if you want, but when reporting problems please mention prominently that megatest failed, include the megatest output, and copy the Charm++ developers at ppl@cs.uiuc.edu on your email. Now you can run the NAMD config script to set up a build directory: ./config ARCH For this specific example: ./config Linux-x86-icc --charm-arch net-linux-tcp-icc This will create a build directory Linux-x86-icc. If you wish to create this directory elsewhere use config DIR/ARCH, replacing DIR with the location the build directory should be created. A symbolic link to the remote directory will be created as well. You can create multiple build directories for the same ARCH by adding a suffix. These can be combined, of course, as in: ./config tcl fftw /tmp/Linux-x86-icc.test1 Now cd to your build directory and type make. The namd2 binary and a number of utilities will be created. If you have trouble building NAMD your compiler may be different from ours. The architecture-specific makefiles in the arch directory use several options to elicit similar behavior on all platforms. Your compiler may conform to an earlier C++ specification than NAMD uses. You compiler may also enforce a later C++ rule than NAMD follows. You may ignore repeated warnings about new and delete matching. The NAMD Wiki at http://www.ks.uiuc.edu/Research/namd/wiki/ has entries on building and running NAMD at various supercomputer centers (e.g., NamdAtTexas) and on various architectures (e.g., NamdOnMPICH). Please consider adding a page on your own porting effort for others to read. ---------------------------------------------------------------------- Memory Usage NAMD has traditionally used less than 100MB of memory even for systems of 100,000 atoms. With the reintroduction of pairlists in NAMD 2.5, however, memory usage for a 100,000 atom system with a 12A cutoff can approach 300MB, and will grow with the cube of the cutoff. This extra memory is distributed across processors during a parallel run, but a single workstation may run out of physical memory with a large system. To avoid this, NAMD now provides a pairlistMinProcs config file option that specifies the minimum number of processors that a run must use before pairlists will be enabled (on fewer processors small local pairlists are generated and recycled rather than being saved, the default is "pairlistMinProcs 1"). This is a per-simulation rather than a compile time option because memory usage is molecule-dependent. ---------------------------------------------------------------------- Improving Parallel Scaling While NAMD is designed to be a scalable program, particularly for simulations of 100,000 atoms or more, at some point adding additional processors to a simulation will provide little or no extra performance. If you are lucky enough to have access to a parallel machine you should measure NAMD's parallel speedup for a variety of processor counts when running your particular simulation. The easiest and most accurate way to do this is to look at the "Benchmark time:" lines that are printed after 20 and 25 cycles (usually less than 500 steps). You can monitor performance during the entire simulation by adding "outputTiming <steps>" to your configuration file, but be careful to look at the "wall time" rather than "CPU time" fields on the "TIMING:" output lines produced. For an external measure of performance, you should run simulations of both 25 and 50 cycles (see the stepspercycle parameter) and base your estimate on the additional time needed for the longer simulation in order to exclude startup costs and allow for initial load balancing. We provide both standard (UDP) and new TCP based precompiled binaries for Linux clusters. We have observed that the TCP version is better on our dual processor clusters with gigabit ethernet while the basic UDP version is superior on our single processor fast ethernet cluster. When using the UDP version with gigabit you can add the +giga option to adjust several tuning parameters. Additional performance may be gained by building NAMD against an SMP version of Charm++ such as net-linux-smp or net-linux-smp-icc. This will use a communication thread for each process to respond to network activity more rapidly. For dual processor clusters we have found it that running two separate processes per node, each with its own communication thread, is faster than using the charmrun ++ppn option to run multiple worker threads. However, we have observed that when running on a single hyperthreaded processor (i.e., a newer Pentium 4) there is an additional 15% boost from running standalone with two threads (namd2 +p2) beyond running two processors (charmrun namd2 ++local +p2). For a cluster of single processor hyperthreaded machines an SMP version should provide very good scaling running one process per node since the communication thread can run very efficiently on the second virtual processor. We are unable to ship an SMP build for Linux due to portability problems with the Linux pthreads implementation needed by Charm++. Extremely short cycle lengths (less than 10 steps) will also limit parallel scaling, since the atom migration at the end of each cycle sends many more messages than a normal force evaluation. Increasing pairlistdist from, e.g., cutoff + 1.5 to cutoff + 2.5, while also doubling stepspercycle from 10 to 20, may increase parallel scaling, but it is important to measure. When increasing stepspercycle, also try increasing pairlistspercycle by the same proportion. NAMD should scale very well when the number of patches (multiply the dimensions of the patch grid) is larger or rougly the same as the number of processors. If this is not the case, it may be possible to improve scaling by adding ``twoAwayX yes'' to the config file, which roughly doubles the number of patches. (Similar options twoAwayY and twoAwayZ also exist, and may be used in combination, but this greatly increases the number of compute objects. twoAwayX has the unique advantage of also improving the scalability of PME.) Additional performance tuning suggestions and options are described at http://www.ks.uiuc.edu/Research/namd/wiki/?NamdPerformanceTuning ---------------------------------------------------------------------- Endian Issues Some architectures write binary data (integer or floating point) with the most significant byte first; others put the most significant byte last. This doesn't effect text files but it does matter when a binary data file that was written on a "big-endian" machine (POWER, PowerPC) is read on a "small-endian" machine (Intel) or vice versa. NAMD generates DCD trajectory files and binary coordinate and velocity files which are "endian-sensitive". While VMD can now read DCD files from any machine and NAMD reads most other-endian binary restart files, many analysis programs (like CHARMM or X-PLOR) require same-endian DCD files. We provide the programs flipdcd and flipbinpdb for switching the endianness of DCD and binary restart files, respectively. These programs use mmap to alter the file in-place and may therefore appear to consume an amount of memory equal to the size of the file. ----------------------------------------------------------------------
footer