Posts by bozz4science

1) Message boards : News : New scientific publication (Message 1489) Posted 6 Oct 2021 by bozz4science Post: Congrats on publishing this exciting journal article! Keep up the good work! I am definitely looking forward to the "many more projects" that you mention :)
2) Message boards : News : Scientific publication and news (Message 1124) Posted 3 Oct 2020 by bozz4science Post: Hey Benoit, that was a very interesting read! Merci beaucoup pour ta vite réponse très informative! I appreciate it very much! Well, your answer covers just about any field that is currently driving innovation in these science domains. I am thrilled that there are so many potential use cases where this tool could be used to help spark further innovation and explorative science. Many of which I haven't even considered before your response. Very exciting future! Considering the second step you are talking about to develop a methodology to filter out the most interesting and relevant molecules that were generated using the de novo molecular generation algorithm, will this be based on machine learning/statistical optimization? The only thing that I was hesitant about first, was that I read somewhere (I believe it was this project's "home" page) that QuChemPedIA was trying to develop an AI system that could potentially develop and optimise yet unknown synthetic molecules with any property you as a researcher desire. I feared that this could potentially be misused and exploited for like let's say weapons research or the like. But in the end I guess, making this tool that is the very product of your research openly available to the public frankly is the right way to proceed, as any innovative solution can eventually be exploited or abused for malicious purpose. And in the end you will still need to require tremendous domain knowledge (in the respective field as well as chemist know-how) to being able to properly handle the tool and get the results you want as well as massive computing power. So there's that. In the end, I enjoyed reading your answer and all the mentioned use cases that could create amazing technical solutions for many of mankind's problem. I love that QuChemPedIA is doing basic methodological science first to create this general purpose tool that can then in return ultimately advance any and every research field that handles "molecules" in some way.
3) Message boards : News : Scientific publication and news (Message 1113) Posted 30 Sep 2020 by bozz4science Post: Well done! Thanks for making all this open to the public. I will have a look at this paper later today even though most of the technical terms in the paper abstract already intimidate me a lot. Anyways, I get the gist of what you are ultimately trying to achieve here and understanding even a little bit more detailed how that is implemented code-wise and some of the minuscule details of what techniques you apply there is just icing on the cake for me :) But I will try my hardest to comprehend the main aspects. Benoit, just one question regarding the forward-looking statements relating to the subsequent articles/papers you mention to be scheduled for 2021/2022. Could you just indulge me what the "top-level" motivation or field is that you are trying to achieve with the development of this particular tool? Maybe you already touched upon this and it slipped my attention, but I would appreciate it anyway if you could tell us if this tool is specifically designed to target the molecule exploration in a particular field/industry or rather like a general-use tool. So far, I couldn't contribute much as I was memory constrained and without a Linux partition on my system, I couldn't exploit the efficiency gains of those native based Linux apps. Hope to ramp it up a bit soon :) Thanks! Again, great work!
4) Questions and Answers : Macintosh : Problem running NWChem application on MacOS (Message 844) Posted 19 May 2020 by bozz4science Post: Thanks Jens for the quick response! Installed the aforementioned version of Virtual Box yesterday but it seems it didn't work out again. Sadly, I experienced similar issues across the board with all VM-based BOINC projects that I run. Starting out just a week ago, every single VM-based project seemed to work just fine, but somehow that changed after upgrading to the latest Virtual box version. (issues with Cosmology@Home, LHC@Home, QuChemPedIA@Home) Had some WUs successfully returned beforehand though. But now error messages are as numerous as tasks that failed such as - Postponed: Communication with VM Hypervisor failed - vsyscall attempted with vsyscall=none - Postponed: VM Hypervisor failed to enter an online state in a timely fashion. Just stumbled across the issue with BOINC-Virtual Box problems in the discussion forums of the respective projects. Seems that this is a rather common one that many other crunchers experience. I'll try various other versions of Virtual Box and hope that some version might work again. Amongst others it was recommend to abort all currently running VM jobs on BOINC. Remove the project, close BOINC manager, install newest version of Virtual Box and reboot. Tried that but didn't work. Without too much of a technical background knowledge I basically already reached my limit here to further look for what is potentially causing this issue. Will try to troubleshoot more on the weekend, but if I don't get it to run stable by then, I'll give up on VM-based projects - at least for now. Thanks again for pointing out this potential issue Jens!
5) Questions and Answers : Macintosh : Problem running NWChem application on MacOS (Message 841) Posted 16 May 2020 by bozz4science Post: Dear community, recently joined QuChemPedIA@home and immediately experienced some issues with running the following task: - od9_athome_b3lyp-321gd,batch85,000857421,nwchem,1581802374 Computer stats: - GenuineIntel Intel(R) Core(TM) i5-4278U CPU @ 2.60GHz [x86 Family 6 Model 69 Stepping 1] - Dual core - INTEL Iris (1536MB) OpenCL: 1.2 - Darwin 19.4.0 - BOINC v 7.16.6 - 8 GB RAM - newest version of VirtualBox installed together with the extension pack This is what the task overview yielded: <core_client_version>7.16.6</core_client_version> <![CDATA[ <stderr_txt> 2020-05-16 13:06:02 (62392): vboxwrapper (7.7.26199): starting 2020-05-16 13:06:03 (62392): Feature: Checkpoint interval offset (292 seconds) 2020-05-16 13:06:03 (62392): Feature: Enabling trickle-ups (Interval: 1800.000000) 2020-05-16 13:06:03 (62392): Detected: VirtualBox VboxManage Interface (Version: 6.1.8) 2020-05-16 13:06:03 (62392): Detected: Sandbox Configuration Enabled 2020-05-16 13:06:03 (62392): Detected: Minimum checkpoint interval (600.000000 seconds) 2020-05-16 13:06:03 (62392): Create VM. (boinc_ca3ab7032117fd5e, slot#9) 2020-05-16 13:06:04 (62392): Setting Memory Size for VM. (1900MB) 2020-05-16 13:06:04 (62392): Setting CPU Count for VM. (1) 2020-05-16 13:06:04 (62392): Setting Chipset Options for VM. 2020-05-16 13:06:04 (62392): Setting Boot Options for VM. 2020-05-16 13:06:04 (62392): Setting Network Configuration for NAT. 2020-05-16 13:06:04 (62392): Disabling VM Network Access. 2020-05-16 13:06:05 (62392): Disabling USB Support for VM. 2020-05-16 13:06:05 (62392): Disabling COM Port Support for VM. 2020-05-16 13:06:05 (62392): Disabling Audio Support for VM. 2020-05-16 13:06:05 (62392): Disabling Clipboard Support for VM. 2020-05-16 13:06:05 (62392): Disabling Drag and Drop Support for VM. 2020-05-16 13:06:05 (62392): Adding storage controller(s) to VM. 2020-05-16 13:06:05 (62392): Adding virtual disk drive to VM. (vm_image.vdi) 2020-05-16 13:06:05 (62392): Adding VirtualBox Guest Additions to VM. 2020-05-16 13:06:06 (62392): Adding network bandwidth throttle group to VM. (Defaulting to 1024GB) 2020-05-16 13:06:06 (62392): Enabling shared directory for VM. 2020-05-16 13:06:06 (62392): Starting VM. (boinc_ca3ab7032117fd5e, slot#9) 2020-05-16 13:06:08 (62392): Successfully started VM. (PID = '62456') 2020-05-16 13:06:08 (62392): Reporting VM Process ID to BOINC. 2020-05-16 13:06:08 (62392): Guest Log: BIOS: VirtualBox 6.1.8 2020-05-16 13:06:08 (62392): Guest Log: CPUID EDX: 0x178bfbff 2020-05-16 13:06:08 (62392): Guest Log: BIOS: ata0-0: PCHS=16383/16/63 LCHS=1024/255/63 2020-05-16 13:06:09 (62392): VM state change detected. (old = 'poweroff', new = 'running') 2020-05-16 13:06:09 (62392): Preference change detected 2020-05-16 13:06:09 (62392): Setting CPU throttle for VM. (66%) 2020-05-16 13:06:09 (62392): Setting checkpoint interval to 600 seconds. (Higher value of (Preference: 180 seconds) or (Vbox_job.xml: 600 seconds)) 2020-05-16 13:06:10 (62392): Guest Log: BIOS: Boot : bseqnr=1, bootseq=0032 2020-05-16 13:06:10 (62392): Guest Log: BIOS: Booting from Hard Disk... 2020-05-16 13:06:14 (62392): Guest Log: BIOS: KBD: unsupported int 16h function 03 2020-05-16 13:06:14 (62392): Guest Log: BIOS: AX=0305 BX=0000 CX=0000 DX=0000 2020-05-16 13:06:15 (62392): VM state change detected. (old = 'running', new = 'paused') 2020-05-16 13:06:26 (62392): VM state change detected. (old = 'paused', new = 'running') 2020-05-16 13:06:29 (62392): Guest Log: vgdrvHeartbeatInit: Setting up heartbeat to trigger every 2000 milliseconds 2020-05-16 13:06:29 (62392): Guest Log: vboxguest: misc device minor 59, IRQ 20, I/O port d020, MMIO at 00000000f0400000 (size 0x400000) 2020-05-16 13:06:50 (62392): Guest Log: vboxsf: g_fHostFeatures=0x8000000f g_fSfFeatures=0x1 g_uSfLastFunction=29 2020-05-16 13:07:06 (62392): VM state change detected. (old = 'running', new = 'paused') 2020-05-16 13:07:28 (62392): VM state change detected. (old = 'paused', new = 'running') 2020-05-16 13:07:33 (62392): Status Report: virtualbox/vboxheadless is no longer running. 2020-05-16 13:07:33 (62392): VM is no longer is a running state. It is in 'poweroff'. 2020-05-16 13:07:33 (62392): VM state change detected. (old = 'running', new = 'poweroff') 2020-05-16 13:07:33 (62392): Powering off VM. 2020-05-16 13:07:33 (62392): Deregistering VM. (boinc_ca3ab7032117fd5e, slot#9) 2020-05-16 13:07:33 (62392): Removing network bandwidth throttle group from VM. 2020-05-16 13:07:33 (62392): Removing storage controller(s) from VM. 2020-05-16 13:07:33 (62392): Removing VM from VirtualBox. 2020-05-16 13:07:33 (62392): Removing virtual disk drive from VirtualBox. 2020-05-16 13:07:39 (62392): Virtual machine exited. 13:07:39 (62392): called boinc_finish(0) </stderr_txt> ]]> Can you point me in the direction of what's causing this issue? Any help is much appreciated. Pls let me know if you need any more information to answer this question. Thx