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technical:whitepaper:start [2022-06-17 12:24] – frey | technical:whitepaper:start [2022-06-17 12:25] (current) – [rJava: when compilers get too smart] frey | ||
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+ | ====== White Papers ====== | ||
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+ | {{ : | ||
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+ | ===== rJava: | ||
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+ | While installing all 16k (nearly 17k) CRAN packages on a recent R 4.1.3 build, many packages with a dependency on rJava would hang when being tested. | ||
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+ | ===== Open MPI, PSM2, and MPI_Comm_spawn() ===== | ||
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+ | The MPI process-spawning API has not been frequently used on our clusters. | ||
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+ | ===== Mellanox UCX and Open MPI on DARWIN ===== | ||
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+ | During early-access testing of the DARWIN cluster several users reported issues with their MPI jobs' crashing unexpectedly in code locations that worked on previous clusters (like Caviness). | ||
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+ | ===== /dev/shm exhaustion ===== | ||
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+ | As time goes by, the ''/ | ||
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+ | ===== R: runtime configurable BLAS/LAPACK ===== | ||
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+ | The R statistical computing software can be built atop a variety of BLAS and LAPACK libraries -- including its own internal //Rblas// and //Rlapack// libraries. | ||
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+ | ===== Mills: threading performance study ===== | ||
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+ | The behavior of the Mills cluster' | ||
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+ | {{: | ||
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+ | ===== Mills: AMD Opteron 6200 Unix Tuning Guide ===== | ||
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+ | The Nodes on the Mills cluster have 2 or 4 AMD Opteron 6200 series sockets. | ||
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+ | This technical tuning guide is intended for " | ||
+ | and developers on a Linux platform who perform application development, | ||
+ | system installation" | ||
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+ | [[http:// | ||
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+ | ===== HPC Challenge Awards Competition at SC Conference ===== | ||
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+ | The SC((The International Conference for High Performance Computing, Networking, Storage and Analysis)) High Performance Computing Challenge includes the benchmarks: | ||
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+ | - HPL measures the floating point rate of execution for solving a linear system of equations | ||
+ | - DGEMM measures the floating point rate of execution of double precision real matrix matrix multiplication | ||
+ | - STREAM measures sustainable memory bandwidth (in GB/s) and the corresponding computation rate for a simple vector kernel | ||
+ | - PTRANS (parallel matrix transpose) exercises communications between pairs of processors. It is a useful test of the total communications capacity of the network. | ||
+ | - Random Access measures the rate of integer random updates of memory (GUPS) | ||
+ | - FFT measures the floating point rate of execution of double precision complex one dimensional Discrete Fourier Transform (DFT) | ||
+ | - Communication bandwidth and latency measures latency and bandwidth of a number of simultaneous communication patterns; based on b_eff (effective bandwidth benchmark). | ||
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+ | [[http:// | ||
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+ | ===== Matlab: Computational threads on a shared cluster ===== | ||
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+ | By default Matlab uses multiple computational threads for standard linear algebra calculations. | ||
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+ | To fully use the computational threads you must call the built in high level functions or data parallel constructs in Matlab. | ||
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+ | ===== Mills: Using ACML In High Performance Computing Challenge ===== | ||
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+ | For Mills, the recommended libraries include OpenMPI, ACML, and FFTW. The AMD recommended compilers include Open64 and PGI. | ||
+ | The following document from AMD includes instructions for installing these libraries, but this is not needed on Mills since they are already installed as VALET packages. | ||
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+ | [[http:// | ||
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+ | ===== Mills: Benchmarking studies ===== | ||
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+ | ==== High Performance Computing Challenge studies ==== | ||
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+ | * [[hpcc open64 acml|open64 compiler with ACML and openmpi libraries]] | ||