Last updated: 2019-10-15
Checks: 7 0
Knit directory: listerlab/
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | 01de06d | davetang | 2019-10-15 | wflow_publish(files = c(“analysis/index.Rmd”, “analysis/stiletto.Rmd”, “analysis/uwa_vm.Rmd”)) |
| html | 21e7535 | davetang | 2019-10-01 | Build site. |
| Rmd | 31e33bb | davetang | 2019-10-01 | wflow_publish(files = c(“analysis/machete.Rmd”, “analysis/stiletto.Rmd”)) |
| html | 140440a | davetang | 2019-09-03 | Build site. |
| Rmd | f6cfac0 | davetang | 2019-09-03 | Using stiletto |
Stiletto has four physical sockets with 12 cores per socket; each CPU supports multi-threading (2 threads) resulting in 4 * 12 * 2 = 96 CPUs.
Architecture: x86_64
CPU op-mode(s): 32-bit, 64-bit
Byte Order: Little Endian
CPU(s): 96
On-line CPU(s) list: 0-95
Thread(s) per core: 2
Core(s) per socket: 12
Socket(s): 4
NUMA node(s): 4
Vendor ID: GenuineIntel
CPU family: 6
Model: 79
Model name: Intel(R) Xeon(R) CPU E5-4640 v4 @ 2.10GHz
Stepping: 1
CPU MHz: 2584.625
CPU max MHz: 2600.0000
CPU min MHz: 1200.0000
BogoMIPS: 4190.42
Virtualization: VT-x
L1d cache: 32K
L1i cache: 32K
L2 cache: 256K
L3 cache: 30720KThere is 1T of memory.
total used free shared buff/cache available
Mem: 1.0T 243G 10G 1.8G 753G 759G
Swap: 11G 10G 216MThe Out of memory (OOM) killer sometimes doesn’t work resulting in a server crash, so please monitor your memory usage.
For your analyses, use the scratch directory; remember clean up scratch after you are done!
/mnt/eql/stiletto-scratchUse the four working directories to store your data. DO NOT USE these directories for long read/write jobs because they are on a network mount (nfs4).
/mnt/remoteserv/switch/userdata/usrdat01
/mnt/remoteserv/switch/userdata/usrdat02
/mnt/remoteserv/switch/userdata/usrdat03
/mnt/remoteserv/switch/userdata/usrdat04tmp directoryThe root directory (/) only has 14G of space, so do not use /tmp as your temporary directory as this will fill up the root directory.
TMPDIR is the canonical environment variable in Unix and POSIX that should be used to specify a temporary directory for scratch space. Most Unix programs will honour this setting and use its value to denote the scratch area for temporary files instead of the common default of /tmp or /var/tmp.
First create your own tmp directory on scratch. Change dtang to your own username.
mkdir -p /mnt/eql/stiletto-scratch/dtang/tmpNext add this line to your .bashrc file.
TMPDIR=/mnt/eql/stiletto-scratch/dtang/tmpIf all goes well, you should see that TMPDIR is set.
source ~/.bashrc
echo $TMPDIR
/mnt/eql/stiletto-scratch/dtang/tmpMost programs will use the TMPDIR environment variable but if they don’t, see if there is an option for manually setting the temporary directory. For example, in the sort program you would use the -T parameter.
sort -T /mnt/eql/stiletto-scratch/dtang/tmp some_fileR compiled in /opt/R. To avoid library conflicts (especially with Anaconda/Miniconda), set PATH to use only the system-wide directories.
#!/bin/bash
# --with-cairo use cairo (and pango) if available [yes]
# --with-libpng use libpng library (if available) [yes]
# --with-jpeglib use jpeglib library (if available) [yes]
# --with-libtiff use libtiff library (if available) [yes]
r_version=3.6.1
# use only system libraries
PATH=/usr/local/bin:/usr/local/sbin:/usr/lib64/qt-3.3/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin
./configure --prefix=/opt/R/$r_version --with-x=yes --enable-R-shlib=yes --with-cairo=yes --with-libpng=yes
make
make installhttps://github.com/guoweilong/cgmaptools
cd /opt/
sudo git clone https://github.com/guoweilong/cgmaptools.git && cd cgmaptools
sudo ./install.shPlease add the following line to your ~/.bash_profile, and source ~/.bash_profile before running cgmaptools.
export PATH=/opt/cgmaptools:$PATH
sessionInfo()R version 3.6.1 (2019-07-05)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Mojave 10.14.6
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib
locale:
[1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] forcats_0.4.0 stringr_1.4.0 dplyr_0.8.3 purrr_0.3.2
[5] readr_1.3.1 tidyr_1.0.0 tibble_2.1.3 ggplot2_3.2.1
[9] tidyverse_1.2.1
loaded via a namespace (and not attached):
[1] Rcpp_1.0.2 cellranger_1.1.0 pillar_1.4.2 compiler_3.6.1
[5] git2r_0.26.1 workflowr_1.4.0 tools_3.6.1 zeallot_0.1.0
[9] digest_0.6.21 lubridate_1.7.4 jsonlite_1.6 evaluate_0.14
[13] lifecycle_0.1.0 nlme_3.1-141 gtable_0.3.0 lattice_0.20-38
[17] pkgconfig_2.0.3 rlang_0.4.0 cli_1.1.0 rstudioapi_0.10
[21] yaml_2.2.0 haven_2.1.1 xfun_0.10 withr_2.1.2
[25] xml2_1.2.2 httr_1.4.1 knitr_1.25 hms_0.5.1
[29] generics_0.0.2 fs_1.3.1 vctrs_0.2.0 rprojroot_1.3-2
[33] grid_3.6.1 tidyselect_0.2.5 glue_1.3.1 R6_2.4.0
[37] readxl_1.3.1 rmarkdown_1.16 modelr_0.1.5 magrittr_1.5
[41] whisker_0.4 backports_1.1.5 scales_1.0.0 htmltools_0.4.0
[45] rvest_0.3.4 assertthat_0.2.1 colorspace_1.4-1 stringi_1.4.3
[49] lazyeval_0.2.2 munsell_0.5.0 broom_0.5.2 crayon_1.3.4