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

Fri Jul 7 17:42:57 EEST 2023

Dear Anders,

I can confirm that I successfully connected from an external network (I am
actually working from home today).

In a few instances when we got similar bug reports, it was indeed a problem
with the firewall on the users side.

Sincerely,
Antanas

On Fri, 7 Jul 2023 at 17:36, Anders Blom <Anders.Blom at synopsys.com> wrote:

> 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> 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>
> *Sent:* Friday, July 7, 2023 15:33
> *To:* Anders Blom <andersb at synopsys.com>
> *Cc:* cod-bugs at ibt.lt; Bo Lue <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> 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
>
>
>
>
>
> 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
> synopsys.com <http://www.synopsys.com/> | 675 Almanor Ave, Sunnyvale, CA
> 94085, USA
>
>
> <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
>
>
>
>
>
> --
>
> Antanas Vaitkus,
>
> Vilnius University,
> Life Sciences Center,
> Institute of Biotechnology,
> room C521, Saulėtekio al. 7,
> LT-10257 Vilnius, Lithuania
>
>
>

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

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