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<title>Copying larger files and large file sets — MIT Satori User Documentation documentation</title>
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<li class="toctree-l2"><a class="reference internal" href="satori-R.html#r-and-python">R and Python</a></li>
<li class="toctree-l2"><a class="reference internal" href="satori-R.html#running-r-in-a-container">Running R in a container</a></li>
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<li class="toctree-l1"><a class="reference internal" href="satori-cuda-aware-mpi.html">Using MPI and CUDA on Satori</a><ul>
<li class="toctree-l2"><a class="reference internal" href="satori-cuda-aware-mpi.html#getting-started">Getting started</a></li>
<li class="toctree-l2"><a class="reference internal" href="satori-cuda-aware-mpi.html#compiling">Compiling</a></li>
<li class="toctree-l2"><a class="reference internal" href="satori-cuda-aware-mpi.html#submiting-a-batch-script">Submiting a batch script</a><ul>
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<li class="toctree-l1"><a class="reference internal" href="satori-relion-cryoem.html">Relion Cryoem for Satorians</a><ul>
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<li class="toctree-l1 current"><a class="current reference internal" href="#">Copying larger files and large file sets</a></li>
<li class="toctree-l1"><a class="reference internal" href="#using-mrsync">Using mrsync</a></li>
<li class="toctree-l1"><a class="reference internal" href="#using-aspera-for-remote-file-transfer-to-satori-cluster">Using Aspera for remote file transfer to Satori cluster</a></li>
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<li class="toctree-l3"><a class="reference internal" href="tips-and-tricks/storage/index.html">How can I see disk usage?</a></li>
<li class="toctree-l3"><a class="reference internal" href="tips-and-tricks/storage/index.html#where-should-i-put-world-or-project-shared-datasets">Where should I put world or project shared datasets?</a></li>
<li class="toctree-l3"><a class="reference internal" href="portal-howto/customization.html">How can I create custom Jupyter kernels for the Satori web portal?</a><ul>
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<li class="toctree-l4"><a class="reference internal" href="tips-and-tricks/sys_queries/index.html#what-linux-distribution-version-am-i-running">What Linux distribution version am I running?</a></li>
<li class="toctree-l4"><a class="reference internal" href="tips-and-tricks/sys_queries/index.html#what-linux-kernel-level-am-i-running">What Linux kernel level am I running?</a></li>
<li class="toctree-l4"><a class="reference internal" href="tips-and-tricks/sys_queries/index.html#what-software-levels-are-installed-on-the-system">What software levels are installed on the system?</a></li>
</ul>
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<li class="toctree-l3"><a class="reference internal" href="tips-and-tricks/sys_queries/index.html#system-hardware-queries">System hardware queries</a><ul>
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<li class="toctree-l3"><a class="reference internal" href="tips-and-tricks/singularity-tips/index.html">How do I build a Singularity image from scratch?</a><ul>
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<li class="toctree-l4"><a class="reference internal" href="tips-and-tricks/singularity-tips/index.html#run-docker-in-ppc64le-mode-on-an-x86-machine-to-generate-an-image-for-satori">Run Docker in ppc64le mode on an x86 machine to generate an image for Satori</a></li>
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<li class="toctree-l4"><a class="reference internal" href="tips-and-tricks/singularity-tips/index.html#using-singularity-instead-of-docker">Using Singularity instead of Docker</a></li>
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<li class="toctree-l4"><a class="reference internal" href="tutorial-examples/eric-fiala-wmlce-notebooks-master/index.html#useful-references">Useful references</a></li>
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<li class="toctree-l3"><a class="reference internal" href="tutorial-examples/unsupervised-learning-on-ocean-ecosystem-model/index.html">Finding clusters in high-dimensional data using tSNE and DB-SCAN</a><ul>
<li class="toctree-l4"><a class="reference internal" href="tutorial-examples/unsupervised-learning-on-ocean-ecosystem-model/index.html#description">Description</a></li>
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<li class="toctree-l4"><a class="reference internal" href="tutorial-examples/unsupervised-learning-on-ocean-ecosystem-model/index.html#code-and-input-data-repositories-for-this-example">Code and input data repositories for this example</a></li>
<li class="toctree-l4"><a class="reference internal" href="tutorial-examples/unsupervised-learning-on-ocean-ecosystem-model/index.html#useful-references">Useful references</a></li>
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<li class="toctree-l3"><a class="reference internal" href="tutorial-examples/biggan-pytorch/index.html">BigGAN-PyTorch</a><ul>
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<li class="toctree-l4"><a class="reference internal" href="tutorial-examples/biggan-pytorch/index.html#commands-to-run-this-example">Commands to run this example</a></li>
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<li class="toctree-l4"><a class="reference internal" href="tutorial-examples/biggan-pytorch/index.html#useful-references">Useful references</a></li>
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<li>Copying larger files and large file sets</li>
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<div class="section" id="copying-larger-files-and-large-file-sets">
<h1>Copying larger files and large file sets<a class="headerlink" href="#copying-larger-files-and-large-file-sets" title="Permalink to this headline">¶</a></h1>
<p>cp command is a single threaded process and it does not take advantage of the distributed file systems like GPFS. If you have a lot of files to copy, or you have very large files, you may want to use one of the large data set copy fasciliities supporte4d by Satori. The two methods are:</p>
<ul class="simple">
<li>msrsync (<a class="reference external" href="https://github.com/jbd/msrsync" target="_blank">https://github.com/jbd/msrsync</a>) whichis a python wrapper around rsync.</li>
<li>Aspera (<a class="reference external" href="https://www.ibm.com/products/aspera" target="_blank">https://www.ibm.com/products/aspera</a>) which is a high speed data transfer service offered by IBM</li>
</ul>
</div>
<div class="section" id="using-mrsync">
<h1>Using mrsync<a class="headerlink" href="#using-mrsync" title="Permalink to this headline">¶</a></h1>
<p><a class="reference external" href="https://github.com/jbd/msrsync" target="_blank">https://github.com/jbd/msrsync</a></p>
<p>To install</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>wget https://raw.githubusercontent.com/jbd/msrsync/master/msrsync <span class="o">&&</span> chmod +x msrsync
</pre></div>
</div>
<p>To use</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>$ msrsync --help
usage: msrsync <span class="o">[</span>options<span class="o">]</span> <span class="o">[</span>--rsync <span class="s2">"rsync-options-string"</span><span class="o">]</span> SRCDIR <span class="o">[</span>SRCDIR2...<span class="o">]</span> DESTDIR
or: msrsync --selftest
msrsync options:
-p, --processes ... number of rsync processes to use <span class="o">[</span><span class="m">1</span><span class="o">]</span>
-f, --files ... limit buckets to <files> files number <span class="o">[</span><span class="m">1000</span><span class="o">]</span>
-s, --size ... limit partitions to BYTES size <span class="o">(</span><span class="m">1024</span> suffixes: K, M, G, T, P, E, Z, Y<span class="o">)</span> <span class="o">[</span>1G<span class="o">]</span>
-b, --buckets ... where to put the buckets files <span class="o">(</span>default: auto temporary directory<span class="o">)</span>
-k, --keep <span class="k">do</span> not remove buckets directory at the end
-j, --show show bucket directory
-P, --progress show progress
--stats show additional stats
-d, --dry-run <span class="k">do</span> not run rsync processes
-v, --version print version
rsync options:
-r, --rsync ... MUST be last option. rsync options as a quoted string <span class="o">[</span><span class="s2">"-aS --numeric-ids"</span><span class="o">]</span>. The <span class="s2">"--from0 --files-from=... --quiet --verbose --stats --log-file=..."</span> options will ALWAYS be added, no
matter what. Be aware that this will affect all rsync *from/filter files <span class="k">if</span> you want to use them. See rsync<span class="o">(</span><span class="m">1</span><span class="o">)</span> manpage <span class="k">for</span> details.
self-test options:
-t, --selftest run the integrated unit and functional tests
-e, --bench run benchmarks
-g, --benchshm run benchmarks <span class="k">in</span> /dev/shm or the directory <span class="k">in</span> <span class="nv">$SHM</span> environment variable
</pre></div>
</div>
<p>Example:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>[root@service0001 kvtran-test]# ./msrsync -p 24 --stats --rsync "-a --inplace" /data/ImageNet/ILSVRC2012 ILSVRC2012-service0001
Status: SUCCESS
Working directory: /nobackup/projects/kvtran-test
Command line: ./msrsync -p 24 --stats --rsync -a --inplace /data/ImageNet/ILSVRC2012 ILSVRC2012-service0001
Total size: 143.1 G
Total entries: 1331169
Buckets number: 1332
Mean entries per bucket: 999
Mean size per bucket: 110.0 M
Entries per second: 3136
Speed: 345.2 M/s
Rsync workers: 24
Total rsync's processes (1332) cumulative runtime: 10116.8s
Crawl time: 212.5s (50.1% of total runtime)
Total time: 424.5s
</pre></div>
</div>
<p>Note:
–inplace: rsync writes updated data directly to a file, instead of making a copy and moving it into place.</p>
<p>We used 24 workers in this example because I found out that gave me the best time when I tested with the GPFS filesystem in POK environment.</p>
<p>The copy time is 424.5s using msrsync versus 27m34.417s with cp command.</p>
<p>For remove the directory,weI used rsync and it took 8 minutes to remove a directory with 1000 subdirectories and total of 1281167 files on POK env.</p>
<p>We created an empty directory and used it with rsync –delete as the example below:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>-bash-4.2$ <span class="nb">time</span> rsync -a --delete empty-dir/ train2-24/
real 8m25.144s
user 0m2.756s
sys 0m35.559s
</pre></div>
</div>
</div>
<div class="section" id="using-aspera-for-remote-file-transfer-to-satori-cluster">
<h1>Using Aspera for remote file transfer to Satori cluster<a class="headerlink" href="#using-aspera-for-remote-file-transfer-to-satori-cluster" title="Permalink to this headline">¶</a></h1>
<p>Note: Aspera server is enabled on either satori-login-001.mit.edu or satori-login-002.mit.edu login nodes.</p>
<ol class="arabic simple">
<li>Install Aspera client or connect on your local machine</li>
</ol>
<ul class="simple">
<li><dl class="first docutils">
<dt>For Mac, Windows or Linux-x86, please download and install Aspera connect from <a class="reference external" href="https://downloads.asperasoft.com/en/downloads/8?list" target="_blank">https://downloads.asperasoft.com/en/downloads/8?list</a></dt><dd>To install on Mac or Windows, please following the software installation step to complete the installation. For Linux as non-root user, untar the gz file and run the install script file. After the installation is complete, it will be located at your home directory .aspera/connect</dd>
</dl>
</li>
<li><dl class="first docutils">
<dt>For PowerPC (ppc64le) system, please download and install Aspera desktop client from <a class="reference external" href="https://downloads.asperasoft.com/en/downloadsArchive/2" target="_blank">https://downloads.asperasoft.com/en/downloadsArchive/2</a></dt><dd>To install desktop client on Power system after download deb or rpm file:</dd>
</dl>
</li>
<li>on an Ubuntu system</li>
</ul>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>sudo apt-get install ibm-aspera-desktopclient-3.9.6.176567-linux-ppc64le.deb
</pre></div>
</div>
<ul class="simple">
<li>RHEL|CentOS</li>
</ul>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>sudo yum install ibm-aspera-desktopclient-3.9.6.176567-linux-ppc64le.rpm
</pre></div>
</div>
<p>2. Transfer files using Aspera connect or client
Note: <asperauser> is your userid on Satori</p>
<ul class="simple">
<li>on Windows</li>
</ul>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>ascp.exe –P <span class="m">22</span> –mode<span class="o">=</span>send<span class="p">|</span>recv <span class="se">\p</span>ath<span class="se">\t</span>o<span class="se">\f</span>ile.txt <asperauser>@satori-login-002.mit.edu:/path/to/file.txt
</pre></div>
</div>
<ul class="simple">
<li>on Mac or Linux</li>
</ul>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>ascp –P 22 –mode=send|recv /path/to/file.txt <asperauser>@satori-login-002.mit.edu:/path/to/file.txt
The path to ascp command is located at $HOME/.aspera/connect/bin
Here's an estimator for Aspera transfer times https://www.ibm.com/aspera/file-transfer-calculator/
</pre></div>
</div>
<p>For technical support, Support <<a class="reference external" href="mailto:satori-support%40techsquare.com" target="_blank">satori-support<span>@</span>techsquare<span>.</span>com</a>></p>
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