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<p class="MsoNormal">Great!<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">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?<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">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. <o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">This is just to eliminate as many possibilities as possible.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Cheers,<o:p></o:p></p>
<p class="MsoNormal">Anders<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><b>From:</b> Antanas Vaitkus <antanas.vaitkus90@gmail.com> <br>
<b>Sent:</b> Friday, July 7, 2023 16:19<br>
<b>To:</b> Anders Blom <andersb@synopsys.com>; Saulius Gražulis <grazulis@ibt.lt><br>
<b>Cc:</b> cod-bugs@ibt.lt; Bo Lue <bolu@synopsys.com><br>
<b>Subject:</b> Re: [Cod-bugs] Unable to connect to SQL server<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt">Dear Anders,<o:p></o:p></p>
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<p class="MsoNormal">I am very glad to hear that your company finds the COD useful. I am not in the position to individually<br>
make high-level policy decisions, but I will definitely forward your email to my supervisor (Saulius Gražulis)<br>
and other members of the COD Advisory Board. Please keep in mind, however, that it may take some time<br>
for them to respond as most of them have other primary work responsibilities.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Please also let us know if you need any additional assistance at resolving the database connection issues on your end.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Sincerely<o:p></o:p></p>
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<p class="MsoNormal">Antanas<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">On Fri, 7 Jul 2023 at 16:54, Anders Blom <<a href="mailto:Anders.Blom@synopsys.com">Anders.Blom@synopsys.com</a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Thank you for the quick response, Antanas. It’s very good to know that the server is working.<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">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.<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">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:
<a href="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$" target="_blank"><font color="red"><b>MailScanner has detected definite fraud in the website at "urldefense.com". Do <i>not</i> trust this website:</b></font>
https://docs.quantumatk.com/tutorials/li_ion_diffusion/li_ion_diffusion.html#import-lifepo4-bulk-structure</a><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">If relevant and interesting to COD, we could perhaps consider making this a more formal partnership, although I have to consult other people on my side in terms of co-marketing
or PR announcements.<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Let me also point out that QuantumATK is essentially free for academic use in Europe, as it is provided via EuroPractice (<a href="https://urldefense.com/v3/__https:/www.europractice.stfc.ac.uk/tools/synopsys_details.html*QATK__;Iw!!A4F2R9G_pg!eVjWKEM8gQXHv0P54cdQdJ_9r6sFDwkt9zOtW5CxaduuK15dCpuumEf4xUPqvfhVg6PBH79PjjYEvmj3APEop5LtXbIJMQ$" target="_blank"><font color="red"><b>MailScanner has detected definite fraud in the website at "urldefense.com". Do <i>not</i> trust this website:</b></font> https://www.europractice.stfc.ac.uk/tools/synopsys_details.html#QATK</a>)
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!<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">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.<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">With thanks, and with hopes for a continued mutually beneficial relationship,<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Anders<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">------------------------------------------------<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><b>Anders Blom, Ph.D.</b><br>
Solutions Engineer, Sr Staff<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">EDAG, Circuit Design & TCAD Solutions<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;margin-bottom:12.0pt">+1 650-584-5000 (ext 47495)
<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><b>From:</b> Antanas Vaitkus <<a href="mailto:antanas.vaitkus90@gmail.com" target="_blank">antanas.vaitkus90@gmail.com</a>>
<br>
<b>Sent:</b> Friday, July 7, 2023 15:33<br>
<b>To:</b> Anders Blom <<a href="mailto:andersb@synopsys.com" target="_blank">andersb@synopsys.com</a>><br>
<b>Cc:</b> <a href="mailto:cod-bugs@ibt.lt" target="_blank">cod-bugs@ibt.lt</a>; Bo Lue <<a href="mailto:bolu@synopsys.com" target="_blank">bolu@synopsys.com</a>><br>
<b>Subject:</b> Re: [Cod-bugs] Unable to connect to SQL server<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;margin-bottom:12.0pt">Dear Anders Blom,<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;margin-bottom:12.0pt">I just tried running your query [1] useing MySQL/MariaDb from my machine and everything<br>
works as expected so the issue is most likely on your end.<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">I also attach a file with the results of the query in case they would prove useful for you in the short term.<o:p></o:p></p>
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[1] mysql -u cod_reader -h <a href="https://urldefense.com/v3/__http:/sql.crystallography.net__;!!A4F2R9G_pg!eWRgu5jS9uWlm2_CBj1I4LlR8nz0Z0XnbZbgrjDsj_B0oeW2Q8r9K4tpNypBOl2WK0gGVYOsnL6SvbLll7PTWDiJUPRYMQ$" target="_blank"><font color="red"><b>MailScanner has detected definite fraud in the website at "urldefense.com". Do <i>not</i> trust this website:</b></font>
sql.crystallography.net</a> -e "select file from data where ((LOWER(formula) RLIKE ' ag') AND (nel = 1))" cod<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">On Fri, 7 Jul 2023 at 16:29, Anders Blom <<a href="mailto:Anders.Blom@synopsys.com" target="_blank">Anders.Blom@synopsys.com</a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Hi COD,<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">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?<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">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<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><img border="0" width="965" height="61" style="width:10.052in;height:.6354in" id="m_-1886887992907579099m_-2962859575026305366Picture_x0020_2" src="cid:image001.png@01D9B0F1.248BD110"><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">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.<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">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).<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Kind regards,<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Anders Blom<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><b> </b><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><b> </b><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">------------------------------------------------<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><b>Anders Blom, Ph.D.</b><br>
Solutions Engineer, Sr Staff<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">EDAG, Circuit Design & TCAD Solutions<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">M: +1 408 874 5806 | W: +1 650 584 5000 (ext 47495) |
<a href="mailto:anders.blom@synopsys.com" target="_blank">anders.blom@synopsys.com</a><br>
<a href="http://www.synopsys.com/" target="_blank">synopsys.com</a> | 675 Almanor Ave, Sunnyvale, CA 94085, USA<o:p></o:p></p>
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<a href="https://www.synopsys.com/silicon/quantumatk.html" target="_blank"><span style="color:windowtext;text-decoration:none"><img border="0" width="400" height="45" style="width:4.1666in;height:.4687in" id="m_-1886887992907579099m_-2962859575026305366Picture_x0020_1" src="cid:image002.png@01D9B0F1.248BD110"></span></a><o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><br>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">_______________________________________________<br>
Cod-bugs mailing list<br>
<a href="mailto:Cod-bugs@lists.crystallography.net" target="_blank">Cod-bugs@lists.crystallography.net</a><br>
<a href="https://urldefense.com/v3/__http:/lists.crystallography.net/cgi-bin/mailman/listinfo/cod-bugs__;!!A4F2R9G_pg!eWRgu5jS9uWlm2_CBj1I4LlR8nz0Z0XnbZbgrjDsj_B0oeW2Q8r9K4tpNypBOl2WK0gGVYOsnL6SvbLll7PTWDhq5hQw9Q$" target="_blank"><font color="red"><b>MailScanner has detected definite fraud in the website at "urldefense.com". Do <i>not</i> trust this website:</b></font> http://lists.crystallography.net/cgi-bin/mailman/listinfo/cod-bugs</a><o:p></o:p></p>
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<span class="m-1886887992907579099gmailsignatureprefix">-- </span><o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Antanas Vaitkus,<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Vilnius University,<br>
Life Sciences Center,<br>
Institute of Biotechnology,<br>
room C521, Saulėtekio al. 7,<br>
LT-10257 Vilnius, Lithuania<o:p></o:p></p>
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<span class="gmailsignatureprefix">-- </span><o:p></o:p></p>
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<p class="MsoNormal">Antanas Vaitkus,<o:p></o:p></p>
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<p class="MsoNormal">Vilnius University,<br>
Life Sciences Center,<br>
Institute of Biotechnology,<br>
room C521, Saulėtekio al. 7,<br>
LT-10257 Vilnius, Lithuania<o:p></o:p></p>
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