diff --git a/docs.it4i/salomon/capacity-computing.md b/docs.it4i/salomon/capacity-computing.md index 18b896440cb841c7a68ec5d9b1e0fdfa58216b3d..aa947db011b4ba820f3736b445e1bb639233ef14 100644 --- a/docs.it4i/salomon/capacity-computing.md +++ b/docs.it4i/salomon/capacity-computing.md @@ -292,7 +292,7 @@ When deciding this values, think about following guiding rules : 1. Number of tasks should be modulo 24. 1. These rules are valid only when all tasks have similar task walltimes T. -### Submit the Job Array +### Submit the Job Array (-J) To submit the job array, use the qsub -J command. The 992 tasks' job of the [example above](capacity-computing/#combined_example) may be submitted like this: diff --git a/docs.it4i/salomon/ib-single-plane-topology.md b/docs.it4i/salomon/ib-single-plane-topology.md index 5ea65562559d028641e2c2019b5e3eaf44f0d4b1..b1a5381e6280b9c1ace1c84c90b12ef2d4641650 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. @@ -16,7 +16,7 @@ Each color in each physical IRU represents one dual-switch ASIC switch.  -### IB Single-Plane Topology - Accelerated Nodes +## IB Single-Plane Topology - Accelerated Nodes Each of the 3 inter-connected D racks are equivalent to one half of M-Cell rack. 18 x D rack with MIC accelerated nodes [r21-r38] are equivalent to 3 M-Cell racks as shown in a diagram [7D Enhanced Hypercube](7d-enhanced-hypercube/). diff --git a/docs.it4i/salomon/software/chemistry/nwchem.md b/docs.it4i/salomon/software/chemistry/nwchem.md index 00bebe9e14c4c57689e8d80266876b92ed69e4d9..a26fc701ee44585dbab1f942685b92d9190adfa5 100644 --- a/docs.it4i/salomon/software/chemistry/nwchem.md +++ b/docs.it4i/salomon/software/chemistry/nwchem.md @@ -1,7 +1,5 @@ # NWChem -**High-Performance Computational Chemistry** - ## Introduction NWChem aims to provide its users with computational chemistry tools that are scalable both in their ability to treat large scientific computational chemistry problems efficiently, and in their use of available parallel computing resources from high-performance parallel supercomputers to conventional workstation clusters. diff --git a/docs.it4i/salomon/software/debuggers/aislinn.md b/docs.it4i/salomon/software/debuggers/aislinn.md index 0b41542cf1d9167ad517cb2a0f788f433efaf942..e1dee28b8d6d78ef7be2371afb2f8884f2b5f364 100644 --- a/docs.it4i/salomon/software/debuggers/aislinn.md +++ b/docs.it4i/salomon/software/debuggers/aislinn.md @@ -8,7 +8,7 @@ !!! note Aislinn is software developed at IT4Innovations and some parts are still considered experimental. If you have any questions or experienced any problems, please contact the author: <mailto:stanislav.bohm@vsb.cz>. -### Usage +## Usage Let us have the following program that contains a bug that is not manifested in all runs: diff --git a/docs.it4i/salomon/software/debuggers/intel-vtune-amplifier.md b/docs.it4i/salomon/software/debuggers/intel-vtune-amplifier.md index 724e4e58a43d7a196544702b601ffa306da7386d..2fdbd18e166d3e553a8ad5719f7945f902cbd73c 100644 --- a/docs.it4i/salomon/software/debuggers/intel-vtune-amplifier.md +++ b/docs.it4i/salomon/software/debuggers/intel-vtune-amplifier.md @@ -90,5 +90,5 @@ You can obtain this command line by pressing the "Command line..." button on Ana ## References 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) +1. [Intel® VTune™ Amplifier Support](https://software.intel.com/en-us/intel-vtune-amplifier-xe-support/documentation) +1. [https://software.intel.com/en-us/amplifier_help_linux](https://software.intel.com/en-us/amplifier_help_linux) diff --git a/docs.it4i/salomon/software/debuggers/total-view.md b/docs.it4i/salomon/software/debuggers/total-view.md index a7642fa193b9d31dd2d4d2c2b974f3c1a79dd769..f4f69278ff59e8f2cd35aad8b5c79bf78a4a0171 100644 --- a/docs.it4i/salomon/software/debuggers/total-view.md +++ b/docs.it4i/salomon/software/debuggers/total-view.md @@ -112,7 +112,9 @@ The source code of this function can be also found in You can also add only following line to you ~/.tvdrc file instead of the entire function: -**source /apps/all/OpenMPI/1.10.1-GNU-4.9.3-2.25/etc/openmpi-totalview.tcl** +```bash +source /apps/all/OpenMPI/1.10.1-GNU-4.9.3-2.25/etc/openmpi-totalview.tcl +``` You need to do this step only once. See also [OpenMPI FAQ entry](https://www.open-mpi.org/faq/?category=running#run-with-tv)