<p>I haven't used canu for several years but looking back at my labbook I ran it with two additional flags:</p>
<p><code>-minThreads=8 -maxThreads=8</code></p>
<p>My memory on the subject is a bit hazy but  think I had to play around with these settings to get it to work.  I also set the flag:</p>
<p><code>-maxMemory=6</code></p>

CC BY-SA 4.0
2022-02-02T21:47:27.733Z
2022-02-02T21:47:27.733Z
Graeme
<p>I am currently running canu on an LSF Linux server using the following script called assemble.sh:</p>
<pre><code>canu -p species -d output genomeSize=100m -pacbio-raw subreads.fastq
</code></pre>
<p>I then submit this script with the following in a computer node:</p>
<pre><code>bsub -q basement -E 'test -e /nfs/users/nfs_c/cr' -R &quot;select[mem&gt;25000] rusage[mem=25000]&quot; -M25000 -o canu.o -e canu.e -J canu 'bash assemble.sh' -n8 -R&quot;span[hosts=1]&quot;
</code></pre>
<p>On my laptop, using 8 cores and 16 GB memory, assemble.sh took about 48h. On the cluster, it's been running for 72h and it is still running. I wonder if I am allocating resources correctly or if I can do something better. On my laptop, I can see in my activity monitor that canu is using many cores at the same time. Do you know how I can check this in an LSF server?</p>
<p><a href="http://canu.readthedocs.io/en/latest/faq.html#faq" rel="nofollow noreferrer">This page</a> talks about submitting jobs on LSF. In particular, it mentions this: <code>gridOptions=&quot;your options list&quot;</code> but I don't know how to use this option.</p>
<p>Any help would be appreciated.</p>
<p>checking the queue with <code>bjobs -u all</code> shows there are 125259 jobs running. My own job is running, it's not pending. Does the number of other jobs affect the running of my own job? I will ask IT if there are preferred writing locations. I did not consider that could change the speed of the job. Do you know a command to check how many resources my job is using?</p>

<assembly><linux><canu>
How to submit a canu job on LSF high-performance computing cluster farm?
# How to submit a canu job on LSF high-performance computing cluster farm?

(Asked by: username_0 on 2017-11-23)

I am currently running canu on an LSF Linux server using the following script called assemble.sh:
canu -p species -d output genomeSize=100m -pacbio-raw subreads.fastq

I then submit this script with the following in a computer node:
bsub -q basement -E 'test -e /nfs/users/nfs_c/cr' -R "select[mem>25000] rusage[mem=25000]" -M25000 -o canu.o -e canu.e -J canu 'bash assemble.sh' -n8 -R"span[hosts=1]"

On my laptop, using 8 cores and 16 GB memory, assemble.sh took about 48h. On the cluster, it's been running for 72h and it is still running. I wonder if I am allocating resources correctly or if I can do something better. On my laptop, I can see in my activity monitor that canu is using many cores at the same time. Do you know how I can check this in an LSF server?
This page talks about submitting jobs on LSF. In particular, it mentions this: gridOptions="your options list" but I don't know how to use this option.
Any help would be appreciated.
checking the queue with bjobs -u all shows there are 125259 jobs running. My own job is running, it's not pending. Does the number of other jobs affect the running of my own job? I will ask IT if there are preferred writing locations. I did not consider that could change the speed of the job. Do you know a command to check how many resources my job is using?

**Tags:** assembly, linux, canu

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## 1 answers

### Answer by username_1 on 2022-02-02. Score: 1

I haven't used canu for several years but looking back at my labbook I ran it with two additional flags:

`-minThreads=8 -maxThreads=8`

My memory on the subject is a bit hazy but think I had to play around with these settings to get it to work. I also set the flag:

`-maxMemory=6`


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