At login, modules commands set up a basic environment for the default compilers, tools, and libraries. For example: the $PATH, $MANPATH, $LIBPATH environment variables, directory locations (e.g., $WORK, $HOME), aliases (e.g., cdw, cdh) and license paths are set by the login modules. Therefore, there is no need for you to set them or update them when updates are made to system and application software.
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The MPI compiler wrappers use the same compilers that are invoked for serial code compilation. So, any of the compiler flags used with the icc command can also be used with mpicc; likewise for ifort and mpif90; and icpc and mpicxx.
TACC's MATLAB, Python, and R modules all use threaded (parallel) MKL as their underlying BLAS/LAPACK library. These means that even serial codes written in MATLAB, Python, or R may benefit from MKL's thread-based parallelism. This requires no action on your part other than specifying an appropriate max thread count for MKL; see the section below for more information.
If you are running a single serial, unthreaded application (or an unthreaded MPI code involving a single MPI task per node) it is usually best to give MKL as much flexibility as possible by setting the max thread count to the total number of hardware threads on the node (16 on Sandy Bridge, 272 on KNL). Of course things are more complicated if you are running more than one process on a node: e.g. multiple serial processes, threaded applications, hybrid MPI-threaded applications, or pure MPI codes running more than one MPI rank per node. See -us/articles/recommended-settings-for-calling-intel-mkl-routines-from-multi-threaded-applications and related Intel resources for examples of how to manage threading when calling MKL from multiple processes.
Each Stampede node (of E5 16 cores, and a Phi coprocessor; and K20 GPUs on gpu nodes) can be assigned to only one user at a time; hence, a complete node is dedicated to a user's job and accrues wall-clock time for 16 cores whether all cores are used or not. The allocation usage is based solely on the E5 core wallclock hours used; the Phi coprocessors and the NVIDIA GPUs are "free" components within the nodes. Codes run in the serial queue will be charged the full rate of 16 cores/node.
This section discusses how to submit jobs for your particular programming model: MPI, hybrid (openMP+MPI), symmetric, and serial codes. Stampede also provides users still experimenting with codes interactive access to the development nodes.
For serial batch executions, use one node and one task, and do not use the ibrun command to launch the executable (just use the executable name) and submit your job to the serial queue (partition). The serial queue has a 12-hour runtime limit and allows up to 6 simultaneous runs per user. There are 148 nodes available for the serial queue.
The other xterm window is black-on-white, and can be used to start both serial programs running on the node hosting the vncserver process, or parallel jobs running across the set of cores associated with the original batch job. Additional xterm windows can be created using the window-manager left-button menu.
VisIt first loads a dataset and presents a dialog allowing for selecting either a serial or parallel engine. Select the parallel engine. Note that this dialog will also present options for the number of processes to start and the number of nodes to use; these options are actually ignored in favor of the options specified when the VNC server job was started.
It may not be a good idea to use all 272 hardware threads simultaneously, and it's certainly not the first thing you should try. In most cases it's best to specify no more than 64-68 MPI tasks or independent processes per node, and 1-2 threads/core. One exception is worth noting: when calling threaded MKL from a serial code, it's safe to set OMP_NUM_THREADS or MKL_NUM_THREADS to 272. This is because MKL will choose an appropriate thread count less than or equal to the value you specify. See Controlling Threading in MKL above for more information. 2ff7e9595c