User 779e37e0e6
10-06-2015 20:26:02
Hi all,
I recently upgraded to JChem version 15.5.25. I used jchem webservices to create (by genrating features such as inchikey, inchi, etc...) and store chemical entities that I then use for different cheminformatics operations, including superstructure search.I do this through sidekiq jobs. The input format for each struture is SMILES.
When I submit one job with >1000 query structures at one time, or sequentially submit many jobs of one more more input queries, two possible scenarios occur:
1) After computing features for a number of input structures, Jchem report errors for the remaining input structures, the computation of inchi and inchikey failed (which is definitely NOT a result of the molecule structure being wrong).
OR
2) After computing features for a number of input structures, and storing them, the remaining input structures are not stored, and neither does JChem compute any of their features.
I use jchem web services hrough Apache Tomcat.
I assume that in both scenarios, JChem crashes. However, I do not know how to deal with this.
Thanks.
Regards,
Yan
ChemAxon 13811e1703
11-06-2015 07:18:05
Hi Yan,
Can you please provide the server logs for us? In case of Tomcat it can be found on path:{CATALINA_HOME}/logs/chemaxon.log
Thanks,
Peter
User 779e37e0e6
11-06-2015 16:52:52
Hi Peter,
Thanks for replying. I have attached a zipped folder with 6 log files. Each corresponds to one server, since the jobs are distributed over the six servers.
Please let me know if you find something.
Thanks
Regards,
Yan
User 779e37e0e6
11-06-2015 22:33:09
Hi Peter,
I also decided to truncate and repopulate the table of my JChem database, which contain the patterns I use for superstructure search. To check the patterns for correctness, I run a few superstructure search everytime I add a new patterns. After adding ~770 patterns, I kept getting Request Timeout errors, and the process could not continue.
I stopped and restarted tomcat. However, it did not help at all.
BTW: what is your email address?
Regards,
User 779e37e0e6
12-06-2015 16:35:51
HI Peter,
Hi all,
Did you manage to find what causes Jchem to stop? I could not find any solution so far.
Regarding my last email, where I mentioned the timeout errors: I tried to insert a pattern through our JChem Web service's web interface.
------------------- This is the query-------
{
"operationType": "INSERT",
"structure": "[$([!C]-[#6](=O)!@-[#6]~1~[#6]~[#6]~[#6]~c2ccccc~12),$([!C]-[#6](=O)!@-c1cccc2~[#6]~[#6]~[#6]~[#6]~c12)]",
"additionalData":{
"name":"test-1"
}
}
----------------This is the error report---------
<!DOCTYPE HTML PUBLIC "-//IETF//DTD HTML 2.0//EN">
<html><head>
<title>502 Proxy Error</title>
</head><body>
<h1>Proxy Error</h1>
<p>The proxy server received an invalid
response from an upstream server.<br />
The proxy server could not handle the request <em><a href="/jchem/rest-v0/data/classyfire/table/patterns/operation">POST /jchem/rest-v0/data/test_db/table/patterns/operation</a></em>.<p>
Reason: <strong>Error reading from remote server</strong></p></p>
<hr>
<address>Apache/2.2.15 (CentOS) Server at jchem.xxx.com Port 80</address>
</body></html>
May be that could help solve the issue regarding the second problem.
Regards,
Yan
ChemAxon 13811e1703
15-06-2015 07:18:43
Hi Yannick,
I tried to contact you on the email address given for you forum profile, please check it, and reply or give another address.
I did not see any errors in the attached log files and also http error 502 is not coming from the application, but can be caused by overloading.
What kind of hardware you are using? How many parallel requests are you sending?
Regards,
Peter
User 779e37e0e6
15-06-2015 17:09:08
Hi Peter,
I saw your e-mail. You can contact me using that address.
I am suprised why it should be overloaded, I have used 20 virtual machines in parrallel before, each of which had 2 CPUs.
Right now, I am using ony 6 virtual machines (on Google Compute) Each of them has an instance of JCHEM, and has 4CPUs (Intel Haswell) /3.6GB, 20GB of disk space.
Regards,
Yannick
User 779e37e0e6
15-06-2015 20:18:33
Hi Peter,
One more question: Does your latest version of JChem work with Java 1.7 or 1.8? I think the memory management on these version is better. If not, are you planning to use Java 1.7 or higher on the next release?
We definitely think that compared to the older versions of jchem we have used, the new version seem to bring quite some issues when it comes to memory. At least, from our end here.
Regards,
Yan
ChemAxon 13811e1703
16-06-2015 07:16:29
Hi Yan,
It should work with both 1.7 and 1.8 versions.
I'm still confused about the crashes you experience, I don't see any error in the log files, can you take a look at the catalina.out for any kind of error?
Regards,
Peter