diff --git a/docs.it4i/anselm-cluster-documentation/software/debuggers/allinea-ddt.md b/docs.it4i/anselm-cluster-documentation/software/debuggers/allinea-ddt.md index 576d46674ebe89458dbba7c39680ff25477a1be5..de7d1da222e3c1c0d1fd32e92eb77513981a4188 100644 --- a/docs.it4i/anselm-cluster-documentation/software/debuggers/allinea-ddt.md +++ b/docs.it4i/anselm-cluster-documentation/software/debuggers/allinea-ddt.md @@ -47,9 +47,8 @@ $ mpif90 -g -O0 -o test_debug test.f Before debugging, you need to compile your code with theses flags: -!!! Note "Note" - \- **g** : Generates extra debugging information usable by GDB. -g3 includes even more debugging information. This option is available for GNU and INTEL C/C++ and Fortran compilers. - +!!! Note + - **g** : Generates extra debugging information usable by GDB. -g3 includes even more debugging information. This option is available for GNU and INTEL C/C++ and Fortran compilers. - **O0** : Suppress all optimizations. ## Starting a Job with DDT diff --git a/docs.it4i/anselm-cluster-documentation/software/debuggers/allinea-performance-reports.md b/docs.it4i/anselm-cluster-documentation/software/debuggers/allinea-performance-reports.md index 6cbed37781d67e3fe6dbd1cdfc2aef91f8fa1af3..fdc57fb37aec104af98ab2a030210c387ef4277f 100644 --- a/docs.it4i/anselm-cluster-documentation/software/debuggers/allinea-performance-reports.md +++ b/docs.it4i/anselm-cluster-documentation/software/debuggers/allinea-performance-reports.md @@ -1,7 +1,5 @@ # Allinea Performance Reports -\##quick application profiling - ## Introduction Allinea Performance Reports characterize the performance of HPC application runs. After executing your application through the tool, a synthetic HTML report is generated automatically, containing information about several metrics along with clear behavior statements and hints to help you improve the efficiency of your runs. @@ -31,7 +29,7 @@ Instead of [running your MPI program the usual way](../mpi/), use the the perf r $ perf-report mpirun ./mympiprog.x ``` -The mpi program will run as usual. The perf-report creates two additional files, in _.txt and _.html format, containing the performance report. Note that [demanding MPI codes should be run within the queue system](../../resource-allocation-and-job-execution/job-submission-and-execution/). +The mpi program will run as usual. The perf-report creates two additional files, in \*.txt and \*.html format, containing the performance report. Note that [demanding MPI codes should be run within the queue system](../../resource-allocation-and-job-execution/job-submission-and-execution/). ## Example diff --git a/docs.it4i/salomon/environment-and-modules.md b/docs.it4i/salomon/environment-and-modules.md index 48b3f4932c5b11bc1cebfeb13926da1ecf11e27a..0a452049bd61f9913449ee45b0c951873777cec9 100644 --- a/docs.it4i/salomon/environment-and-modules.md +++ b/docs.it4i/salomon/environment-and-modules.md @@ -26,9 +26,6 @@ fi !!! Note "Note" Do not run commands outputting to standard output (echo, module list, etc) in .bashrc for non-interactive SSH sessions. It breaks fundamental functionality (scp, PBS) of your account! Take care for SSH session interactivity for such commands as stated in the previous example. -How to using modules in examples: -<tty-player controls src=/src/salomon/modules_salomon.ttyrec></tty-player> - ### Application Modules In order to configure your shell for running particular application on Salomon we use Module package interface. diff --git a/docs.it4i/salomon/ib-single-plane-topology.md b/docs.it4i/salomon/ib-single-plane-topology.md index e37cdf4b3f2f2a7a869a0ce101284269a65c23ba..d654fe45c9f7d0a504eadcd12984f1533007dcb3 100644 --- a/docs.it4i/salomon/ib-single-plane-topology.md +++ b/docs.it4i/salomon/ib-single-plane-topology.md @@ -8,7 +8,7 @@ The SGI ICE X IB Premium Blade provides the first level of interconnection via d - 3 ports on each chip provide connectivity between the chips - 24 ports from each switch chip connect to the external bulkhead, for a total of 48 -\###IB single-plane topology - ICEX M-Cell +### IB single-plane topology - ICEX M-Cell Each color in each physical IRU represents one dual-switch ASIC switch. diff --git a/docs.it4i/salomon/job-priority.md b/docs.it4i/salomon/job-priority.md index c6c97a5e9e59dde966ad173936208152f7ddd4c6..e98d56b7f5aa405c5384aa712ef7505c41b33e6a 100644 --- a/docs.it4i/salomon/job-priority.md +++ b/docs.it4i/salomon/job-priority.md @@ -29,8 +29,8 @@ Fair-share priority is calculated as  where MAX_FAIRSHARE has value 1E6, -usage_Project_ is cumulated usage by all members of selected project, -usage_Total_ is total usage by all users, by all projects. +usage<sub>Project</sub> is cumulated usage by all members of selected project, +usage<sub>Total</sub> is total usage by all users, by all projects. Usage counts allocated core-hours (`ncpus x walltime`). Usage is decayed, or cut in half periodically, at the interval 168 hours (one week). @@ -41,7 +41,7 @@ Usage counts allocated core-hours (`ncpus x walltime`). Usage is decayed, or cut Calculated fair-share priority can be also seen as Resource_List.fairshare attribute of a job. -\###Eligible time +### Eligible time Eligible time is amount (in seconds) of eligible time job accrued while waiting to run. Jobs with higher eligible time gains higher priority. diff --git a/docs.it4i/salomon/job-submission-and-execution.md b/docs.it4i/salomon/job-submission-and-execution.md index 83e7c6f9d5a4db2a7c256c2f86635e665ec9a857..0087bb6f0be3ff92906ae41dbdafeccd3ee5a22b 100644 --- a/docs.it4i/salomon/job-submission-and-execution.md +++ b/docs.it4i/salomon/job-submission-and-execution.md @@ -257,7 +257,7 @@ Job ID Username Queue Jobname SessID NDS TSK Memory Time S Time 16547.isrv5 user2 qprod job3x 13516 2 32 -- 48:00 R 00:58 ``` -In this example user1 and user2 are running jobs named job1, job2 and job3x. The jobs job1 and job2 are using 4 nodes, 16 cores per node each. The job1 already runs for 38 hours and 25 minutes, job2 for 17 hours 44 minutes. The job1 already consumed 64_38.41 = 2458.6 core hours. The job3x already consumed 0.96_32 = 30.93 core hours. These consumed core hours will be accounted on the respective project accounts, regardless of whether the allocated cores were actually used for computations. +In this example user1 and user2 are running jobs named job1, job2 and job3x. The jobs job1 and job2 are using 4 nodes, 16 cores per node each. The job1 already runs for 38 hours and 25 minutes, job2 for 17 hours 44 minutes. The job1 already consumed 64 x 38.41 = 2458.6 core hours. The job3x already consumed 0.96 x 32 = 30.93 core hours. These consumed core hours will be accounted on the respective project accounts, regardless of whether the allocated cores were actually used for computations. Check status of your jobs using check-pbs-jobs command. Check presence of user's PBS jobs' processes on execution hosts. Display load, processes. Display job standard and error output. Continuously display (tail -f) job standard or error output. diff --git a/docs.it4i/salomon/software/debuggers/allinea-performance-reports.md b/docs.it4i/salomon/software/debuggers/allinea-performance-reports.md index ec39904bb166d31f8f181aa8a66c738d02359ad3..526f28cc89d5fd41c2ef5cd220a3475d8bc58f54 100644 --- a/docs.it4i/salomon/software/debuggers/allinea-performance-reports.md +++ b/docs.it4i/salomon/software/debuggers/allinea-performance-reports.md @@ -28,7 +28,7 @@ Instead of [running your MPI program the usual way](../mpi/mpi/), use the the pe $ perf-report mpirun ./mympiprog.x ``` -The mpi program will run as usual. The perf-report creates two additional files, in _.txt and _.html format, containing the performance report. Note that demanding MPI codes should be run within [ the queue system](../../resource-allocation-and-job-execution/job-submission-and-execution/). +The mpi program will run as usual. The perf-report creates two additional files, in \*.txt and \*.html format, containing the performance report. Note that demanding MPI codes should be run within [ the queue system](../../resource-allocation-and-job-execution/job-submission-and-execution/). ## Example diff --git a/docs.it4i/salomon/software/debuggers/intel-vtune-amplifier.md b/docs.it4i/salomon/software/debuggers/intel-vtune-amplifier.md index 3007857498d13233c3d9b0d229ab62c4f30cc40f..2733d42c28012a51499056d129adc3fc456fd31d 100644 --- a/docs.it4i/salomon/software/debuggers/intel-vtune-amplifier.md +++ b/docs.it4i/salomon/software/debuggers/intel-vtune-amplifier.md @@ -2,7 +2,7 @@ ## Introduction -Intel_® _VTune™ Amplifier, part of Intel Parallel studio, is a GUI profiling tool designed for Intel processors. It offers a graphical performance analysis of single core and multithreaded applications. A highlight of the features: +Intel *®* VTune™ Amplifier, part of Intel Parallel studio, is a GUI profiling tool designed for Intel processors. It offers a graphical performance analysis of single core and multithreaded applications. A highlight of the features: - Hotspot analysis - Locks and waits analysis @@ -62,11 +62,11 @@ It is possible to analyze both native and offloaded Xeon Phi applications. ### Native mode -This mode is useful for native Xeon Phi applications launched directly on the card. In _Analysis Target_ window, select _Intel Xeon Phi coprocessor (native), _choose path to the binary and MIC card to run on. +This mode is useful for native Xeon Phi applications launched directly on the card. In *Analysis Target* window, select *Intel Xeon Phi coprocessor (native)*, choose path to the binary and MIC card to run on. ### Offload mode -This mode is useful for applications that are launched from the host and use offload, OpenCL or mpirun. In _Analysis Target_ window, select _Intel Xeon Phi coprocessor (native), _choose path to the binaryand MIC card to run on. +This mode is useful for applications that are launched from the host and use offload, OpenCL or mpirun. In *Analysis Target* window, select *Intel Xeon Phi coprocessor (native)*, choose path to the binaryand MIC card to run on. !!! Note "Note" If the analysis is interrupted or aborted, further analysis on the card might be impossible and you will get errors like "ERROR connecting to MIC card". In this case please contact our support to reboot the MIC card. @@ -89,6 +89,6 @@ You can obtain this command line by pressing the "Command line..." button on Ana ## References -1. <https://www.rcac.purdue.edu/tutorials/phi/PerformanceTuningXeonPhi-Tullos.pdf> Performance Tuning for Intel® Xeon Phi™ Coprocessors -2. <https://software.intel.com/en-us/intel-vtune-amplifier-xe-support/documentation> >Intel® VTune™ Amplifier Support -3. <https://software.intel.com/en-us/amplifier_help_linux> +1. [Performance Tuning for Intel® Xeon Phi™ Coprocessors](https://www.rcac.purdue.edu/tutorials/phi/PerformanceTuningXeonPhi-Tullos.pdf) +2. [Intel® VTune™ Amplifier Support](https://software.intel.com/en-us/intel-vtune-amplifier-xe-support/documentation) +3. [https://software.intel.com/en-us/amplifier_help_linux](https://software.intel.com/en-us/amplifier_help_linux)