Hi guys, I&#39;m fairly new to cloud computing and about 2 days in to using cloudman for galaxy...<br><div class="gmail_quote"><div><br><div>I have setup a m2.4xlarge master node and flexible load for up to 4 workers of the m2.xlarge type, minimum one.</div>


<div>I was able to upload 6 samples of paired end RNAseq-&gt;12 files, gz file sizes around 5-8 gb.</div><div>Grooming files took about a day, but my previous experience was on an in-house Galaxy install which was pretty small so I didn&#39;t think of anything at the time.</div>


<div>I started 3 Tophat jobs and I noticed the UI being a bit sluggish to respond, added a 4th one hoping it might push it over the edge for the worker nodes.</div><div><br></div><div>Unfortunately, 12 hours later, the Tophats are still running, the master node is way over 100%, and the worker is reported idle.</div>


<div>While the cluster log has a few errors in it, it ends saying that the instance for the worker node is ready, despite it encountering errors adding it to the SGE host, code1.</div><div><br></div><div>Has anyone run into this before or has any insight to fixing this? I&#39;m pasting the lower portion of the status log below.</div>


<div><br></div><div>Thanks very much for any help! (Also, several other emails about cloud installs were directed to /dev. If that&#39;s not the right place for this question, I apologize and can change to the /user list.)</div>


<div><div>-- <br>Brian Lin<br><a href="mailto:contact@brian-lin.com" target="_blank">contact@brian-lin.com</a><br><a href="mailto:brian.lin@tufts.edu" target="_blank">brian.lin@tufts.edu</a></div><div><br></div><div><br>

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<div><br></div><div><br></div><div><br></div><div><div>13:15:38 - Instance &#39;i-e2bb0491&#39; reported alive</div><div>13:15:38 - Sent master public key to worker instance &#39;i-e2bb0491&#39;.</div><div>13:15:54 - Adding instance i-e2bb0491 as SGE administrative host.</div>


<div>13:16:06 - Adding instance &#39;i-e2bb0491&#39; to SGE execution host list.</div><div>13:16:11 - Process encountered problems adding instance &#39;i-e2bb0491&#39; as an SGE execution host. Process returned code 1</div>


<div>13:16:26 - Waiting on worker instance &#39;i-e2bb0491&#39; to configure itself...</div><div>13:17:05 - Instance &#39;i-e2bb0491&#39; (IP: 23.23.24.81) ready</div><div>13:42:23 - Rebooting instance i-e2bb0491 (reboot #3).</div>


<div>13:44:27 - Instance &#39;i-e2bb0491&#39; reported alive</div><div>13:44:27 - Sent master public key to worker instance &#39;i-e2bb0491&#39;.</div><div>13:44:56 - Adding instance i-e2bb0491 as SGE administrative host.</div>


<div>13:44:56 - Adding instance &#39;i-e2bb0491&#39; to SGE execution host list.</div><div>13:44:56 - Process encountered problems adding instance &#39;i-e2bb0491&#39; as an SGE execution host. Process returned code 1</div>


<div>13:44:56 - Waiting on worker instance &#39;i-e2bb0491&#39; to configure itself...</div><div>13:46:09 - Instance &#39;i-e2bb0491&#39; (IP: 23.23.24.81) ready</div><div>15:19:37 - Rebooting instance i-e2bb0491 (reboot #4).</div>


<div>15:21:16 - Instance &#39;i-e2bb0491&#39; reported alive</div><div>15:21:16 - Sent master public key to worker instance &#39;i-e2bb0491&#39;.</div><div>15:21:38 - Adding instance i-e2bb0491 as SGE administrative host.</div>


<div>15:21:44 - Adding instance &#39;i-e2bb0491&#39; to SGE execution host list.</div><div>15:21:48 - Process encountered problems adding instance &#39;i-e2bb0491&#39; as an SGE execution host. Process returned code 1</div>


<div>15:21:51 - Waiting on worker instance &#39;i-e2bb0491&#39; to configure itself...</div><div>15:22:13 - Instance &#39;i-e2bb0491&#39; (IP: 23.23.24.81) ready</div><div>15:54:32 - Instance i-e2bb0491 not responding after 4 reboots. Terminating instance.</div>


<div>15:54:32 - Terminating instance i-e2bb0491</div><div>15:54:35 - Instance &#39;i-e2bb0491&#39; removed from the internal instance list.</div><div>15:56:10 - Adding 1 on-demand instance(s)</div><div>15:56:14 - Cannot get cloud instance object without an instance ID?</div>


<div>15:58:26 - Instance &#39;i-98932deb&#39; reported alive</div><div>15:58:26 - Sent master public key to worker instance &#39;i-98932deb&#39;.</div><div>15:59:02 - Adding instance i-98932deb as SGE administrative host.</div>


<div>15:59:09 - Adding instance &#39;i-98932deb&#39; to SGE execution host list.</div><div>15:59:17 - Successfully added instance &#39;i-98932deb&#39; to SGE</div><div>15:59:17 - Waiting on worker instance &#39;i-98932deb&#39; to configure itself...</div>


<div>15:59:46 - Instance &#39;i-98932deb&#39; (IP: 54.234.100.22) ready</div><div>16:12:47 - Rebooting instance i-98932deb (reboot #1).</div><div>16:12:47 - Rebooting instance i-98932deb (reboot #1).</div><div>16:12:47 - Rebooting instance i-98932deb (reboot #1).</div>


<div>16:14:06 - Instance &#39;i-98932deb&#39; reported alive</div><div>16:14:06 - Sent master public key to worker instance &#39;i-98932deb&#39;.</div><div>16:14:29 - Adding instance i-98932deb as SGE administrative host.</div>


<div>16:14:29 - Adding instance &#39;i-98932deb&#39; to SGE execution host list.</div><div>16:14:29 - Process encountered problems adding instance &#39;i-98932deb&#39; as an SGE execution host. Process returned code 1</div>


<div>16:14:29 - Waiting on worker instance &#39;i-98932deb&#39; to configure itself...</div><div>16:14:39 - Instance &#39;i-98932deb&#39; (IP: 54.234.100.22) ready</div></div>
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