[Cod-bugs] {Disarmed} RE: Unable to connect to SQL server

Fri Jul 7 17:36:17 EEST 2023

Great!

For the connection issue, would you mind confirming that you are not on the same network where the SQL server is located? Or, put differently, can you also connect to it when you are e.g. at home? And do you know of other people around the world that actively use the SQL connection?

The point is, I suspect that there is a firewall blocking my request, but I don’t know if it’s my corporate one, or the one at the COD end. So even if you can connect from inside the firewall (if that is the case), it may still be that the SQL server is not responding to outside requests.

This is just to eliminate as many possibilities as possible.

Cheers,
Anders

From: Antanas Vaitkus <antanas.vaitkus90 at gmail.com>
Sent: Friday, July 7, 2023 16:19
To: Anders Blom <andersb at synopsys.com>; Saulius Gražulis <grazulis at ibt.lt>
Cc: cod-bugs at ibt.lt; Bo Lue <bolu at synopsys.com>
Subject: Re: [Cod-bugs] Unable to connect to SQL server

Dear Anders,
I am very glad to hear that your company finds the COD useful. I am not in the position to individually
make high-level policy decisions, but I will definitely forward your email to my supervisor (Saulius Gražulis)
and other members of the COD Advisory Board. Please keep in mind, however, that it may take some time
for them to respond as most of them have other primary work responsibilities.

Please also let us know if you need any additional assistance at resolving the database connection issues on your end.

Sincerely
Antanas

On Fri, 7 Jul 2023 at 16:54, Anders Blom <Anders.Blom at synopsys.com<mailto:Anders.Blom at synopsys.com>> wrote:
Thank you for the quick response, Antanas. It’s very good to know that the server is working.

Let me give some context also on this. I work for the team that develops the atomic-scale modeling tool QuantumATK for DFT and other simulations. The company was QuantumWise earlier, before being acquired in 2017 by Synopsys.

We have for several years provided an interface to COD in our GUI, which allows users to build relatively advanced queries with a few clicks, and then retrieve and directly use structures from COD in their simulations. An example is shown in one of our tutorials: https://docs.quantumatk.com/tutorials/li_ion_diffusion/li_ion_diffusion.html#import-lifepo4-bulk-structure<https://urldefense.com/v3/__https:/docs.quantumatk.com/tutorials/li_ion_diffusion/li_ion_diffusion.html*import-lifepo4-bulk-structure__;Iw!!A4F2R9G_pg!eVjWKEM8gQXHv0P54cdQdJ_9r6sFDwkt9zOtW5CxaduuK15dCpuumEf4xUPqvfhVg6PBH79PjjYEvmj3APEop5L_LAV4IQ$>

If relevant and interesting to COD, we could perhaps consider making this a more formal partnership, although I have to consult other people on my side in terms of co-marketing or PR announcements.

Let me also point out that QuantumATK is essentially free for academic use in Europe, as it is provided via EuroPractice (https://www.europractice.stfc.ac.uk/tools/synopsys_details.html#QATK<https://urldefense.com/v3/__https:/www.europractice.stfc.ac.uk/tools/synopsys_details.html*QATK__;Iw!!A4F2R9G_pg!eVjWKEM8gQXHv0P54cdQdJ_9r6sFDwkt9zOtW5CxaduuK15dCpuumEf4xUPqvfhVg6PBH79PjjYEvmj3APEop5LtXbIJMQ$>) for a cost of only ~€100 per year for a practically unlimited license. We would be delighted if you would consider promoting QuantumATK to your friends and colleagues – our DFT-LCAO code is particularly useful for large-scale simulations of 1000+ atoms, even with HSE, and recently we have taken big steps towards automating fitting of machine-learned MTP forcefields!

So, now I just have to figure out if there are some special firewall rules that need to be set for it to work from at least our own internal network.

With thanks, and with hopes for a continued mutually beneficial relationship,
Anders

------------------------------------------------
Anders Blom, Ph.D.
Solutions Engineer, Sr Staff
EDAG, Circuit Design & TCAD Solutions
+1 650-584-5000 (ext 47495)

From: Antanas Vaitkus <antanas.vaitkus90 at gmail.com<mailto:antanas.vaitkus90 at gmail.com>>
Sent: Friday, July 7, 2023 15:33
To: Anders Blom <andersb at synopsys.com<mailto:andersb at synopsys.com>>
Cc: cod-bugs at ibt.lt<mailto:cod-bugs at ibt.lt>; Bo Lue <bolu at synopsys.com<mailto:bolu at synopsys.com>>
Subject: Re: [Cod-bugs] Unable to connect to SQL server

Dear Anders Blom,
I just tried running your query [1] useing MySQL/MariaDb from my machine and everything
works as expected so the issue is most likely on your end.
I also attach a file with the results of the query in case they would prove useful for you in the short term.

[1] mysql -u cod_reader -h sql.crystallography.net<https://urldefense.com/v3/__http:/sql.crystallography.net__;!!A4F2R9G_pg!eWRgu5jS9uWlm2_CBj1I4LlR8nz0Z0XnbZbgrjDsj_B0oeW2Q8r9K4tpNypBOl2WK0gGVYOsnL6SvbLll7PTWDiJUPRYMQ$> -e "select file from data where ((LOWER(formula) RLIKE ' ag') AND (nel = 1))" cod

On Fri, 7 Jul 2023 at 16:29, Anders Blom <Anders.Blom at synopsys.com<mailto:Anders.Blom at synopsys.com>> wrote:
Hi COD,

I am trying to connect and query the COD database via MySQL, but it is not working. Are you aware of any problems on your end?

I have tried multiple clients, such as pymysql, mysql command line, Oracle MySQLshell and DBeaver GUI. In each case I am able to establish some initial connection, but ultimately it just times out

[cid:image001.png at 01D9B0F1.248BD110]

I say “establish connection” in the sense that if I use incorrect server parameters such as the wrong port or hostname, it fails immediately, whereas with the correct COD hostname and port it does wait until the timeout before showing the above error.

If this is a problem with your server, I hope it can be resolved, whereas if you believe the database is functioning properly for queries like this, then I have to dig further on my end (firewalls, perhaps, although I have tried multiple networks as well).

Kind regards,
Anders Blom

------------------------------------------------
Anders Blom, Ph.D.
Solutions Engineer, Sr Staff
EDAG, Circuit Design & TCAD Solutions
M: +1 408 874 5806 | W: +1 650 584 5000 (ext 47495) | anders.blom at synopsys.com<mailto:anders.blom at synopsys.com>
synopsys.com<http://www.synopsys.com/> | 675 Almanor Ave, Sunnyvale, CA 94085, USA

[cid:image002.png at 01D9B0F1.248BD110]<https://www.synopsys.com/silicon/quantumatk.html>

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Antanas Vaitkus,
Vilnius University,
Life Sciences Center,
Institute of Biotechnology,
room C521, Saulėtekio al. 7,
LT-10257 Vilnius, Lithuania

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Antanas Vaitkus,
Vilnius University,
Life Sciences Center,
Institute of Biotechnology,
room C521, Saulėtekio al. 7,
LT-10257 Vilnius, Lithuania

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