diff --git a/doc.zih.tu-dresden.de/docs/software/modules.md b/doc.zih.tu-dresden.de/docs/software/modules.md index ed92fb518f263c2c8ef0ea6e34880282d1c797b5..6a709c0ce6fdd7e4a1bf1b3217f7947cfaf4a3ca 100644 --- a/doc.zih.tu-dresden.de/docs/software/modules.md +++ b/doc.zih.tu-dresden.de/docs/software/modules.md @@ -30,20 +30,20 @@ see all topics and their available module files. If you just wish to see the ins certain module, you can use `module avail softwarename` and it will display the available versions of `softwarename` only. -## Module environments +## Module Environments On the ZIH systems, there exist different module environments, each containing a set of software modules. -They are activated via the meta module modenv which has different versions, one of which is loaded +They are activated via the meta module `modenv` which has different versions, one of which is loaded by default. You can switch between them by simply loading the desired modenv-version, e.g.: -``` +```console marie@compute$ module load modenv/ml ``` ### modenv/scs5 (default) * SCS5 software -* usually optimized for Intel processors (Partitions: haswell, broadwell, gpu2, julia) +* usually optimized for Intel processors (Partitions: `haswell`, `broadwell`, `gpu2`, `julia`) ### modenv/ml @@ -70,12 +70,11 @@ The command `module spider <modname>` allows searching for specific software in environments. It will also display information on how to load a found module when giving a precise module (with version) as the parameter. -## Per-architecture builds +## Per-architecture Builds Since we have a heterogeneous cluster, we do individual builds of some of the software for each architecture present. This ensures that, no matter what partition the software runs on, a build -optimized for the host architecture is used automatically. This is achieved by having -'/sw/installed' symlinked to different directories on the compute nodes. +optimized for the host architecture is used automatically. For that purpose we have created symbolic links at the system path '/sw/installed' on the compute nodes. However, not every module will be available for each node type or partition. Especially when introducing new hardware to the cluster, we do not want to rebuild all of the older module versions @@ -84,7 +83,7 @@ and in some cases cannot fall-back to a more generic build either. That's why we ### Example Invocation of ml_arch_avail -``` +```console marie@compute$ ml_ar:qLch_avail CP2K Example output: @@ -112,12 +111,12 @@ In order to use your own module files please use the command that are searched by lmod (i.e. the `module` command). You may use a directory `privatemodules` within your home or project directory to setup your own module files. -Please see the [Environment Modules open source project's webpage](http://modules.sourceforge.net/) -for futher information on writing module files. +Please see the [Environment Modules open source project's web page](http://modules.sourceforge.net/) +for further information on writing module files. ### 1. Create Directories -``` +```console marie@compute$ cd $HOME marie@compute$ mkdir --verbose --parents privatemodules/testsoftware marie@compute$ cd privatemodules/testsoftware @@ -127,7 +126,7 @@ marie@compute$ cd privatemodules/testsoftware ### 2. Notify lmod -``` +```console marie@compute$ module use $HOME/privatemodules ``` @@ -137,7 +136,7 @@ marie@compute$ module use $HOME/privatemodules Create a file with the name `1.0` with a test software in the `testsoftware` directory you created earlier -(use e.g. echo, emacs, etc) +(using your favorite editor) and paste the following text into it: ``` #%Module###################################################################### @@ -171,9 +170,9 @@ Check the availability of the module with `ml av`, the output should look like t ### 5. Load Module -Load the test module with `module load testsoftware`, the output: +Load the test module with `module load testsoftware`, the output should look like this: -``` +```console Load testsoftware version 1.0 Module testsoftware/1.0 loaded. ``` @@ -188,7 +187,7 @@ The module files have to be stored in your global projects directory above. To use a project-wide module file you have to add the path to the module file to the module environment with the command -``` +```console marie@compute$ module use /projects/p_projectname/privatemodules ``` @@ -202,5 +201,5 @@ basis. This is the reason why we urge users to store (large) temporary data (lik on the /scratch filesystem or at local scratch disks. **Please note**: We have set `ulimit -c 0` as a default to prevent users from filling the disk with -the dump of a crashed program. bash -users can use `ulimit -Sc unlimited` to enable the debugging -via analyzing the core file (limit coredumpsize unlimited for tcsh). +the dump of crashed programs. `bash` users can use `ulimit -Sc unlimited` to enable the debugging +via analyzing the core file. diff --git a/doc.zih.tu-dresden.de/wordlist.aspell b/doc.zih.tu-dresden.de/wordlist.aspell index 038262ca7b5a4418ceefb66b0d14f57d61582609..2c02aa2042571fdd2bfb9b96ef72a949c352282f 100644 --- a/doc.zih.tu-dresden.de/wordlist.aspell +++ b/doc.zih.tu-dresden.de/wordlist.aspell @@ -1,302 +1,308 @@ -personal_ws-1.1 en 203 +personal_ws-1.1 en 203 +APIs +AVX Abaqus Altix Amber Amdahl's -analytics -anonymized -APIs -AVX -BeeGFS -benchmarking BLAS -broadwell -bsub -bullx +BeeGFS CCM -ccNUMA -centauri -CentOS -cgroups -checkpointing -Chemnitz -citable CLI -conda CPU CPUID CPUs -css CSV CUDA -cuDNN CXFS -dask -dataframes -DataFrames -datamover -DataParallel +CentOS +Chemnitz DDP DDR DFG -DistributedDataParallel DMTCP DNS +DataFrames +DataParallel +DistributedDataParallel +DockerHub Dockerfile Dockerfiles -DockerHub -dockerized -EasyBuild -ecryptfs -engl -english -env EPYC -Espresso ESSL -fastfs +EasyBuild +Espresso FFT FFTW -filesystem -filesystems -Flink FMA -foreach +Flink Fortran -Galilei -Gauss -Gaussian GBit GDDR GFLOPS -gfortran +GPU +GPUs +GROMACS +Galilei +Gauss +Gaussian GiB -gifferent GitHub GitLab GitLab's -glibc -gnuplot -GPU -GPUs -GROMACS -hadoop -haswell HBM HDF HDFS HDFView -Horovod -hostname -Hostnames HPC HPE HPL -html -hyperparameter -hyperparameters -hyperthreading -icc -icpc -ifort +Horovod +Hostnames +IPs +ISA ImageNet Infiniband -inode -IPs Itanium -jobqueue -jpg -jss Jupyter JupyterHub JupyterLab -Keras KNL +Keras LAMMPS LAPACK -lapply LINPACK -linter Linter LoadLeveler -localhost -lsf -lustre -markdownlint -Mathematica -MathKernel -MathWorks -matlab MEGWARE -MiB MIMD -Miniconda -mkdocs MKL MNIST +MathKernel +MathWorks +Mathematica +MiB +Miniconda Montecito -mountpoint -mpi -mpicc -mpiCC -mpicxx -mpif -mpifort -mpirun -multicore -multithreaded -Multithreading MultiThreading +Multithreading NAMD -natively -nbsp -nbsp NCCL -Neptun NFS NGC NRINGS NUMA NUMAlink -NumPy -Nutzungsbedingungen -Nvidia NVLINK NVMe NWChem +Neptun +NumPy +Nutzungsbedingungen +Nvidia OME -OmniOpt OPARI +OmniOpt OpenACC OpenBLAS OpenCL OpenGL OpenMP -openmpi OpenMPI OpenSSH Opteron +PAPI +PESSL +PGI +PMI +PSOCK +Pandarallel +Perf +PiB +Pika +PowerAI +Pre +Preload +Pthreads +Quantum +README +RHEL +RSA +RSS +RStudio +Rmpi +Rsync +Runtime +SFTP +SGEMM +SGI +SHA +SHMEM +SLES +SMP +SMT +SSHFS +STAR +SUSE +SXM +Sandybridge +Saxonid +ScaDS +ScaLAPACK +Scalasca +SciPy +Scikit +Slurm +SubMathKernel +Superdome +TBB +TCP +TFLOPS +TensorBoard +TensorFlow +Theano +ToDo +Trition +VASP +VMSize +VMs +VPN +Vampir +VampirTrace +VampirTrace's +VirtualGL +WebVNC +WinSCP +Workdir +XArray +XGBoost +XLC +XLF +Xeon +Xming +ZIH +ZIH's +analytics +anonymized +benchmarking +broadwell +bsub +bullx +ccNUMA +centauri +cgroups +checkpointing +citable +conda +css +cuDNN +dask +dataframes +datamover +dockerized +ecryptfs +engl +english +env +fastfs +filesystem +filesystems +foreach +gfortran +gifferent +glibc +gnuplot +hadoop +haswell +hiera +hostname +html +hyperparameter +hyperparameters +hyperthreading +icc +icpc +ifort +inode +jobqueue +jpg +jss +lapply +linter +lmod +localhost +lsf +lustre +markdownlint +matlab +mkdocs +modenv +modenvs +modulefile +mountpoint +mpi +mpiCC +mpicc +mpicxx +mpif +mpifort +mpirun +multicore +multithreaded +natively +nbsp +nbsp +openmpi overfitting pandarallel -Pandarallel -PAPI parallelization parallelize parfor pdf -Perf -PESSL -PGI -PiB -Pika pipelining -PMI png -PowerAI ppc pre -Pre -Preload preloaded preloading -PSOCK -Pthreads pymdownx -Quantum queue randint reachability -README reproducibility requeueing -RHEL -Rmpi rome romeo -RSA -RSS -RStudio -Rsync runnable runtime -Runtime salloc -Sandybridge -Saxonid sbatch -ScaDS scalable -ScaLAPACK -Scalasca scancel -Scikit -SciPy scontrol scp scs -SFTP -SGEMM -SGI -SHA -SHMEM -SLES -Slurm -SMP -SMT squeue srun ssd -SSHFS -STAR stderr stdout subdirectories subdirectory -SubMathKernel -Superdome -SUSE -SXM -TBB -TCP -TensorBoard -TensorFlow -TFLOPS -Theano tmp todo -ToDo toolchain toolchains tracefile tracefiles transferability -Trition unencrypted uplink userspace -Vampir -VampirTrace -VampirTrace's -VASP vectorization venv virtualenv -VirtualGL -VMs -VMSize -VPN -WebVNC -WinSCP -Workdir workspace workspaces -XArray -Xeon -XGBoost -XLC -XLF -Xming yaml zih -ZIH -ZIH's