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<p>Dear QE users,</p>
<p>I have srun problem on ubuntu 16.04 cluster with intel mpi. Could
you please me to check what is going on? Thank you!<br>
</p>
<p>
<meta http-equiv="content-type" content="text/html; charset=utf-8">
</p>
<p style="margin: 0px 0px 1em; padding: 0px; border: 0px; font-size:
15px; clear: both; color: rgb(17, 17, 17); font-family: Ubuntu,
Arial, "libra sans", sans-serif; font-style: normal;
font-variant-ligatures: normal; font-variant-caps: normal;
font-weight: normal; letter-spacing: normal; orphans: 2;
text-align: left; text-indent: 0px; text-transform: none;
white-space: normal; widows: 2; word-spacing: 0px;
-webkit-text-stroke-width: 0px; background-color: rgb(255, 255,
255);">I am trying to install slurm in a cluster running ubuntu
16.04.</p>
<p style="margin: 0px 0px 1em; padding: 0px; border: 0px; font-size:
15px; clear: both; color: rgb(17, 17, 17); font-family: Ubuntu,
Arial, "libra sans", sans-serif; font-style: normal;
font-variant-ligatures: normal; font-variant-caps: normal;
font-weight: normal; letter-spacing: normal; orphans: 2;
text-align: left; text-indent: 0px; text-transform: none;
white-space: normal; widows: 2; word-spacing: 0px;
-webkit-text-stroke-width: 0px; background-color: rgb(255, 255,
255);">I am using intel mpi and the installation directory is
located at the head node /opt/intel/impi_5.01.</p>
<p style="margin: 0px 0px 1em; padding: 0px; border: 0px; font-size:
15px; clear: both; color: rgb(17, 17, 17); font-family: Ubuntu,
Arial, "libra sans", sans-serif; font-style: normal;
font-variant-ligatures: normal; font-variant-caps: normal;
font-weight: normal; letter-spacing: normal; orphans: 2;
text-align: left; text-indent: 0px; text-transform: none;
white-space: normal; widows: 2; word-spacing: 0px;
-webkit-text-stroke-width: 0px; background-color: rgb(255, 255,
255);">According to the slurm instruction, it needs to export the
libpmi.so variable.<span class="Apple-converted-space"> </span><a
href="https://slurm.schedmd.com/mpi_guide.html#intel_mpi"
rel="nofollow noreferrer" style="margin: 0px; padding: 0px;
border: 0px; font-size: 15px; color: rgb(150, 45, 12);
text-decoration: none; cursor: pointer;"><a class="moz-txt-link-freetext" href="https://slurm.schedmd.com/mpi_guide.html#intel_mpi">https://slurm.schedmd.com/mpi_guide.html#intel_mpi</a></a></p>
<p style="margin: 0px 0px 1em; padding: 0px; border: 0px; font-size:
15px; clear: both; color: rgb(17, 17, 17); font-family: Ubuntu,
Arial, "libra sans", sans-serif; font-style: normal;
font-variant-ligatures: normal; font-variant-caps: normal;
font-weight: normal; letter-spacing: normal; orphans: 2;
text-align: left; text-indent: 0px; text-transform: none;
white-space: normal; widows: 2; word-spacing: 0px;
-webkit-text-stroke-width: 0px; background-color: rgb(255, 255,
255);">But, I installed slurm-llnl via ubuntu</p>
<pre style="margin: 0px 0px 1em; padding: 5px; border: 0px; font-size: 13px; width: auto; max-height: 600px; overflow: auto; font-family: Consolas, Menlo, Monaco, "Lucida Console", "Liberation Mono", "DejaVu Sans Mono", "Bitstream Vera Sans Mono", "Courier New", monospace, sans-serif; background-color: rgb(239, 240, 241); word-wrap: normal; color: rgb(17, 17, 17); font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: 2; text-align: left; text-indent: 0px; text-transform: none; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px;"><code style="margin: 0px; padding: 0px; border: 0px; font-size: 13px; font-family: Consolas, Menlo, Monaco, "Lucida Console", "Liberation Mono", "DejaVu Sans Mono", "Bitstream Vera Sans Mono", "Courier New", monospace, sans-serif; background-color: rgb(239, 240, 241); white-space: inherit;">sudo apt-get slurm-llnl
</code></pre>
<p style="margin: 0px 0px 1em; padding: 0px; border: 0px; font-size:
15px; clear: both; color: rgb(17, 17, 17); font-family: Ubuntu,
Arial, "libra sans", sans-serif; font-style: normal;
font-variant-ligatures: normal; font-variant-caps: normal;
font-weight: normal; letter-spacing: normal; orphans: 2;
text-align: left; text-indent: 0px; text-transform: none;
white-space: normal; widows: 2; word-spacing: 0px;
-webkit-text-stroke-width: 0px; background-color: rgb(255, 255,
255);">and I am not sure where the libpmi.so is located? So, I did
a search and found a file here, is this the file I'm looking for?</p>
<pre style="margin: 0px 0px 1em; padding: 5px; border: 0px; font-size: 13px; width: auto; max-height: 600px; overflow: auto; font-family: Consolas, Menlo, Monaco, "Lucida Console", "Liberation Mono", "DejaVu Sans Mono", "Bitstream Vera Sans Mono", "Courier New", monospace, sans-serif; background-color: rgb(239, 240, 241); word-wrap: normal; color: rgb(17, 17, 17); font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: 2; text-align: left; text-indent: 0px; text-transform: none; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px;"><code style="margin: 0px; padding: 0px; border: 0px; font-size: 13px; font-family: Consolas, Menlo, Monaco, "Lucida Console", "Liberation Mono", "DejaVu Sans Mono", "Bitstream Vera Sans Mono", "Courier New", monospace, sans-serif; background-color: rgb(239, 240, 241); white-space: inherit;">/usr/lib/x86_64-linux-gnu/libpmi.so
</code></pre>
<p style="margin: 0px 0px 1em; padding: 0px; border: 0px; font-size:
15px; clear: both; color: rgb(17, 17, 17); font-family: Ubuntu,
Arial, "libra sans", sans-serif; font-style: normal;
font-variant-ligatures: normal; font-variant-caps: normal;
font-weight: normal; letter-spacing: normal; orphans: 2;
text-align: left; text-indent: 0px; text-transform: none;
white-space: normal; widows: 2; word-spacing: 0px;
-webkit-text-stroke-width: 0px; background-color: rgb(255, 255,
255);">Anyway, I export the variable and I tried</p>
<pre style="margin: 0px 0px 1em; padding: 5px; border: 0px; font-size: 13px; width: auto; max-height: 600px; overflow: auto; font-family: Consolas, Menlo, Monaco, "Lucida Console", "Liberation Mono", "DejaVu Sans Mono", "Bitstream Vera Sans Mono", "Courier New", monospace, sans-serif; background-color: rgb(239, 240, 241); word-wrap: normal; color: rgb(17, 17, 17); font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: 2; text-align: left; text-indent: 0px; text-transform: none; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px;"><code style="margin: 0px; padding: 0px; border: 0px; font-size: 13px; font-family: Consolas, Menlo, Monaco, "Lucida Console", "Liberation Mono", "DejaVu Sans Mono", "Bitstream Vera Sans Mono", "Courier New", monospace, sans-serif; background-color: rgb(239, 240, 241); white-space: inherit;">srun -p old -N3 -n24 hostname
</code></pre>
<p style="margin: 0px 0px 1em; padding: 0px; border: 0px; font-size:
15px; clear: both; color: rgb(17, 17, 17); font-family: Ubuntu,
Arial, "libra sans", sans-serif; font-style: normal;
font-variant-ligatures: normal; font-variant-caps: normal;
font-weight: normal; letter-spacing: normal; orphans: 2;
text-align: left; text-indent: 0px; text-transform: none;
white-space: normal; widows: 2; word-spacing: 0px;
-webkit-text-stroke-width: 0px; background-color: rgb(255, 255,
255);">It returns,</p>
<pre style="margin: 0px 0px 1em; padding: 5px; border: 0px; font-size: 13px; width: auto; max-height: 600px; overflow: auto; font-family: Consolas, Menlo, Monaco, "Lucida Console", "Liberation Mono", "DejaVu Sans Mono", "Bitstream Vera Sans Mono", "Courier New", monospace, sans-serif; background-color: rgb(239, 240, 241); word-wrap: normal; color: rgb(17, 17, 17); font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: 2; text-align: left; text-indent: 0px; text-transform: none; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px;"><code style="margin: 0px; padding: 0px; border: 0px; font-size: 13px; font-family: Consolas, Menlo, Monaco, "Lucida Console", "Liberation Mono", "DejaVu Sans Mono", "Bitstream Vera Sans Mono", "Courier New", monospace, sans-serif; background-color: rgb(239, 240, 241); white-space: inherit;">rolly@head:~$ srun -p old -N3 -n24 hostname
node02
node02
node02
node02
node02
node02
node02
node02
node01
node01
head
head
node01
head
head
head
node01
node01
head
node01
head
head
node01
node01
</code></pre>
<p style="margin: 0px 0px 1em; padding: 0px; border: 0px; font-size:
15px; clear: both; color: rgb(17, 17, 17); font-family: Ubuntu,
Arial, "libra sans", sans-serif; font-style: normal;
font-variant-ligatures: normal; font-variant-caps: normal;
font-weight: normal; letter-spacing: normal; orphans: 2;
text-align: left; text-indent: 0px; text-transform: none;
white-space: normal; widows: 2; word-spacing: 0px;
-webkit-text-stroke-width: 0px; background-color: rgb(255, 255,
255);">It appears working.</p>
<p style="margin: 0px 0px 1em; padding: 0px; border: 0px; font-size:
15px; clear: both; color: rgb(17, 17, 17); font-family: Ubuntu,
Arial, "libra sans", sans-serif; font-style: normal;
font-variant-ligatures: normal; font-variant-caps: normal;
font-weight: normal; letter-spacing: normal; orphans: 2;
text-align: left; text-indent: 0px; text-transform: none;
white-space: normal; widows: 2; word-spacing: 0px;
-webkit-text-stroke-width: 0px; background-color: rgb(255, 255,
255);">But as I run my task,</p>
<pre style="margin: 0px 0px 1em; padding: 5px; border: 0px; font-size: 13px; width: auto; max-height: 600px; overflow: auto; font-family: Consolas, Menlo, Monaco, "Lucida Console", "Liberation Mono", "DejaVu Sans Mono", "Bitstream Vera Sans Mono", "Courier New", monospace, sans-serif; background-color: rgb(239, 240, 241); word-wrap: normal; color: rgb(17, 17, 17); font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: 2; text-align: left; text-indent: 0px; text-transform: none; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px;"><code style="margin: 0px; padding: 0px; border: 0px; font-size: 13px; font-family: Consolas, Menlo, Monaco, "Lucida Console", "Liberation Mono", "DejaVu Sans Mono", "Bitstream Vera Sans Mono", "Courier New", monospace, sans-serif; background-color: rgb(239, 240, 241); white-space: inherit;">srun -p old -N3 -n24 ~/QE530-CPU/espresso-5.3.0/bin/pw.x
</code></pre>
<p style="margin: 0px 0px 1em; padding: 0px; border: 0px; font-size:
15px; clear: both; color: rgb(17, 17, 17); font-family: Ubuntu,
Arial, "libra sans", sans-serif; font-style: normal;
font-variant-ligatures: normal; font-variant-caps: normal;
font-weight: normal; letter-spacing: normal; orphans: 2;
text-align: left; text-indent: 0px; text-transform: none;
white-space: normal; widows: 2; word-spacing: 0px;
-webkit-text-stroke-width: 0px; background-color: rgb(255, 255,
255);">It produced errors,</p>
<pre style="margin: 0px 0px 1em; padding: 5px; border: 0px; font-size: 13px; width: auto; max-height: 600px; overflow: auto; font-family: Consolas, Menlo, Monaco, "Lucida Console", "Liberation Mono", "DejaVu Sans Mono", "Bitstream Vera Sans Mono", "Courier New", monospace, sans-serif; background-color: rgb(239, 240, 241); word-wrap: normal; color: rgb(17, 17, 17); font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: 2; text-align: left; text-indent: 0px; text-transform: none; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px;"><code style="margin: 0px; padding: 0px; border: 0px; font-size: 13px; font-family: Consolas, Menlo, Monaco, "Lucida Console", "Liberation Mono", "DejaVu Sans Mono", "Bitstream Vera Sans Mono", "Courier New", monospace, sans-serif; background-color: rgb(239, 240, 241); white-space: inherit;">mpiexec_node02: cannot connect to local mpd (/tmp/mpd2.console_rolly); possible causes:
1. no mpd is running on this host
2. an mpd is running but was started without a "console" (-n option)
mpiexec_node02: cannot connect to local mpd (/tmp/mpd2.console_rolly); possible causes:
1. no mpd is running on this host
2. an mpd is running but was started without a "console" (-n option)
mpiexec_node01: cannot connect to local mpd (/tmp/mpd2.console_rolly); possible causes:
1. no mpd is running on this host
2. an mpd is running but was started without a "console" (-n option)
mpiexec_node01: cannot connect to local mpd (/tmp/mpd2.console_rolly); possible causes:
1. no mpd is running on this host
2. an mpd is running but was started without a "console" (-n option)
mpiexec_node02: cannot connect to local mpd (/tmp/mpd2.console_rolly); possible causes:
1. no mpd is running on this host
2. an mpd is running but was started without a "console" (-n option)
mpiexec_node02: cannot connect to local mpd (/tmp/mpd2.console_rolly); possible causes:
1. no mpd is running on this host
2. an mpd is running but was started without a "console" (-n option)
mpiexec_node02: cannot connect to local mpd (/tmp/mpd2.console_rolly); possible causes:
1. no mpd is running on this host
2. an mpd is running but was started without a "console" (-n option)
mpiexec_node02: cannot connect to local mpd (/tmp/mpd2.console_rolly); possible causes:
1. no mpd is running on this host
2. an mpd is running but was started without a "console" (-n option)
mpiexec_node02: cannot connect to local mpd (/tmp/mpd2.console_rolly); possible causes:
1. no mpd is running on this host
2. an mpd is running but was started without a "console" (-n option)
mpiexec_node01: cannot connect to local mpd (/tmp/mpd2.console_rolly); possible causes:
1. no mpd is running on this host
2. an mpd is running but was started without a "console" (-n option)
mpiexec_node01: cannot connect to local mpd (/tmp/mpd2.console_rolly); possible causes:
1. no mpd is running on this host
2. an mpd is running but was started without a "console" (-n option)
mpiexec_node02: cannot connect to local mpd (/tmp/mpd2.console_rolly); possible causes:
1. no mpd is running on this host
2. an mpd is running but was started without a "console" (-n option)
mpiexec_node01: cannot connect to local mpd (/tmp/mpd2.console_rolly); possible causes:
1. no mpd is running on this host
2. an mpd is running but was started without a "console" (-n option)
mpiexec_node01: cannot connect to local mpd (/tmp/mpd2.console_rolly); possible causes:
1. no mpd is running on this host
2. an mpd is running but was started without a "console" (-n option)
mpiexec_node01: cannot connect to local mpd (/tmp/mpd2.console_rolly); possible causes:
1. no mpd is running on this host
2. an mpd is running but was started without a "console" (-n option)
mpiexec_node01: cannot connect to local mpd (/tmp/mpd2.console_rolly); possible causes:
1. no mpd is running on this host
2. an mpd is running but was started without a "console" (-n option)
</code></pre>
<p style="margin: 0px 0px 1em; padding: 0px; border: 0px; font-size:
15px; clear: both; color: rgb(17, 17, 17); font-family: Ubuntu,
Arial, "libra sans", sans-serif; font-style: normal;
font-variant-ligatures: normal; font-variant-caps: normal;
font-weight: normal; letter-spacing: normal; orphans: 2;
text-align: left; text-indent: 0px; text-transform: none;
white-space: normal; widows: 2; word-spacing: 0px;
-webkit-text-stroke-width: 0px; background-color: rgb(255, 255,
255);">I believe the error prompts are due to running mpiexec with
intel-mpi, it should be using mpirun instead.</p>
<p style="margin: 0px 0px 1em; padding: 0px; border: 0px; font-size:
15px; clear: both; color: rgb(17, 17, 17); font-family: Ubuntu,
Arial, "libra sans", sans-serif; font-style: normal;
font-variant-ligatures: normal; font-variant-caps: normal;
font-weight: normal; letter-spacing: normal; orphans: 2;
text-align: left; text-indent: 0px; text-transform: none;
white-space: normal; widows: 2; word-spacing: 0px;
-webkit-text-stroke-width: 0px; background-color: rgb(255, 255,
255);">
<meta http-equiv="content-type" content="text/html; charset=utf-8">
<span style="color: rgb(17, 17, 17); font-family: Ubuntu, Arial,
"libra sans", sans-serif; font-size: 13px; font-style:
normal; font-variant-ligatures: normal; font-variant-caps:
normal; font-weight: normal; letter-spacing: normal; orphans: 2;
text-align: left; text-indent: 0px; text-transform: none;
white-space: normal; widows: 2; word-spacing: 0px;
-webkit-text-stroke-width: 0px; background-color: rgb(255, 255,
255); display: inline !important; float: none;"><tt>I can
confirm that by exporting the environmental variable, export
I_MPI_PMI_LIBRARY=/usr/lib/x86_64-linux-gnu/libpmi.so, kills
the mpirun. if this is set, mpirun -n 24 -ppn 8 -f
~/machines.LINUX ~/QE530-CPU/espresso-5.3.0/bin/pw.x fails. If
it is removed, mpirun works again.</tt><br>
</span></p>
<p style="margin: 0px 0px 1em; padding: 0px; border: 0px; font-size:
15px; clear: both; color: rgb(17, 17, 17); font-family: Ubuntu,
Arial, "libra sans", sans-serif; font-style: normal;
font-variant-ligatures: normal; font-variant-caps: normal;
font-weight: normal; letter-spacing: normal; orphans: 2;
text-align: left; text-indent: 0px; text-transform: none;
white-space: normal; widows: 2; word-spacing: 0px;
-webkit-text-stroke-width: 0px; background-color: rgb(255, 255,
255);">How can I correct the problem?</p>
<meta http-equiv="content-type" content="text/html; charset=utf-8">
<pre class="moz-signature" cols="72">--
PhD. Research Fellow,
Dept. of Physics & Materials Science,
City University of Hong Kong
Tel: +852 3442 4000
Fax: +852 3442 0538</pre>
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