12 Sep

Publications 2018-2019

Thanks to everyone that reported your publications supported by the UPR HPCf. From October 2018 to September 2019 we supported 45 publications!

Please remember the HPCf runs mainly with external funding, please acknowledge our active awards. You can use

Research reported in this publication was supported by National Institute for General Medical Sciences (NIGMS) of the National Institutes of Health under award number P20GM103475. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.

7 publications with PMCID Complete & Acknowledge HPCf or INBRE grant

  1. Vélez V, Carrasquillo K, Santini J, Ramos Y, Vázquez L, Roche A, Rodríguez J, Parés E. Modelling and molecular docking studies of the cytoplasmic domain of Wsc-family, full-length Ras2p, and therapeutic antifungal compounds. Comput Biol Chem. 2019 Feb; 78:338-352 PMCID: PMC6377308. (BIRC, ADM & CRI) Impact Factor: 1.41
  2. Chorna N.E., Chornyy A.P. (2019) Metabolomics Analysis of Glutamate Receptor Function. In: Burger C., Velardo M. (eds) Glutamate Receptors. Methods in Molecular Biology, vol 1941. Humana Press, New York, NY. PMCID: PMC6413523 (BIRC, CRI) Book Chapter
  3. Forestier-Román IS, López-Rivas A, Sánchez-Vázquez MM, Rohena-Rivera K,Nieves-Burgos G, Ortiz-Zuazaga H, Torres-Ramos CA, Martínez-Ferrer M. Andrographolide induces DNA damage in prostate cancer cells. Oncotarget. 2019 Feb 1;10(10):1085-1101. doi: 10.18632/oncotarget.26628. eCollection 2019 Feb 1. PubMed PMID: 30800220; PubMed Central PMCID: PMC6383681. Impact Factor: 4.78
  4. Pedraza-Marrón CDR, Silva R, Deeds J, Van Belleghem SM, Mastretta-Yanes A, Domínguez-Domínguez O, Rivero-Vega RA, Lutackas L, Murie D, Parkyn D, Bullock LH, Foss K, Ortiz-Zuazaga H, Narváez-Barandica J, Acero A, Gomes G, Betancur-R R. Genomics overrules mitochondrial DNA, siding with morphology on a controversial case of species delimitation. Proc Biol Sci. 2019 Apr 10;286(1900):20182924. doi:10.1098/rspb.2018.2924. PubMed PMID: 30940064; PubMed Central PMCID: PMC6501682. Impact Factor: 4.30
  5. Ribeiro E, Davis AM, Rivero-Vega RA, Ortí G, Betancur-R R. Post-Cretaceous bursts of evolution along the benthic-pelagic axis in marine fishes. Proc Biol Sci. 2018 Dec 19;285(1893):20182010. doi: 10.1098/rspb.2018.2010. PubMed PMID: 30963906; PubMed Central PMCID: PMC6304066 Impact Factor: 4.30
  6. Pagán-Jiménez M, Ruiz-Calderón JF, Dominguez-Bello MG, García-Arrarás JE. Characterization of the intestinal microbiota of the sea cucumber Holothuria glaberrima. PLoS One. 2019 Jan 30;14(1):e0208011. doi:10.1371/journal.pone.0208011. eCollection 2019. PubMed PMID: 30699110; PubMed Central PMCID: PMC6353073. (BIRC, DRPP, CRI) Impact Factor: 2.77
  7. Morales-Ortíz J, Deal V, Reyes F, Maldonado-Martínez G, Ledesma N, Staback F, Croft C, Pacheco A, Ortiz-Zuazaga H, Yost CC, Rowley JW, Madera B, John AS, Chen
  8. J, Lopez J, Rondina MT, Hunter R, Gibson A, Washington AV. Platelet-derived TLT-1 is a prognostic indicator in ALI/ARDS and prevents tissue damage in the lungs in a mouse model. Blood. 2018 Dec 6;132(23):2495-2505. doi:10.1182/blood-2018-03-841593. Epub 2018 Oct 3. PubMed PMID: 30282800; PubMed Central PMCID: PMC6284217. (BIRC, ADM) Impact Factor: 16.52

3 Publications with PMCID in process that acknowledge HPCf or INBRE

  1. Rincon-Sandoval M, Betancur-R R, Maldonado-Ocampo JA. Comparative phylogeography of trans-Andean freshwater fishes based on genome-wide nuclear and mitochondrial markers. Mol Ecol. 2019 Mar;28(5):1096-1115. doi:10.1111/mec.15036. PubMed PMID: 30714250. Impact Factor: 5.85
  2. Betancur-R R, Arcila D, Vari RP, Hughes LC, Oliveira C, Sabaj MH, Ortí G. Phylogenomic incongruence, hypothesis testing, and taxonomic sampling: The monophyly of characiform fishes. Evolution. 2019 Feb;73(2):329-345. doi: 10.1111/evo.13649. Epub 2018 Dec 4. PubMed PMID: 30426469 Impact Factor: 3.57
  3. Yan Gao,a Yuee Xie,a Yuanping Chen, Jinxing Gub and Zhongfang Chen. Spindle nodal chain in three-dimensional α′ boron. Phys. Chem. Chem. Phys., 2018,20, 23500-23506. PMID: 30183022 Impact Factor: 3.56

9 Publications that acknowledge HPCf or INBRE

  1. D. Derilus, A. Forestil, J. Fortuné, O. Polyanska, C. Louime, G. Gervais, and S. E. Massey. (2019). Functional Metagenomics Characterization of an Anaerobic Saltwater Bioreactor. Journal of Renewable Energy Volume 2019, Article ID 4527628. https://doi.org/10.1155/2019/4527628 Impact Factor: 1.51
  2. Shijun YuanHui, DingJinlan Wang, Zhongfang Chen. Extraordinary Magnetoresistance in Janus Monolayer MoTeB2: A Theoretical Prediction. 2018. J. Phys. Chem. C20181224928423-28430. Impact Factor: 2.83
  3. Gu, J., Magagula, S., Zhao, J., Chen, Z., Boosting ORR/OER Activity of Graphdiyne by Simple Heteroatom Doping. Small Methods 2019, 1800550. https://doi.org/10.1002/smtd.201800550. Impact Factor: 8.64
  4. Xiangyu Guo, Jinxing Gu, Xuemin Hu, Shengli Zhang, Zhongfang Chen, Shiping Huang, Coordination tailoring towards efficient single-atom catalysts for N2 fixation: A case study of iron-nitrogen-carbon (Fe@N-C) systems, Catalysis Today, 2019. Impact Factor: 4.88
  5. Sandra C. Albarracín-Suazo, Yomaira J. Pagán-Torres, and María C. Curet-Arana. DFT Study on the Effect of Aluminum Position in Zn-Exchanged MFI on Methane Activation. The Journal of Physical Chemistry C 2019 123 (26), 16164-16171 DOI: 10.1021/acs.jpcc.9b02487. Impact Factor: 2.83
  6. Brian D. Montejo-Valencia and María C. Curet-Arana. Periodic DFT Study of the Opening of Fructose and Glucose Rings and the Further Conversion of Fructose to Trioses Catalyzed by M-BEA (M = Sn, Ti, Zr, or Hf). The Journal of Physical Chemistry C. 2019 123 (6), 3532-3540. DOI: 10.1021/acs.jpcc.8b10211 Impact Factor: 2.83
  7. Jovadell Cruz, Luis Raúl Pericchi. 2018. Sequential Bayesian Tests and the Hypothesis of independent or naive Bayes. Rev. Fac. Cienc., Volumen 7, Número 1, p. 112-123, 2018. ISSN electrónico 2357-5549. ISSN impreso 0121-747X. DOI: https://doi.org/10.15446/rev.fac.cienc.v7n1.67107
  8. Zhao, Y., Zhang, J.‐J., Yuan, S., Chen, Z., Nonvolatile Electrical Control and Heterointerface‐Induced Half‐Metallicity of 2D Ferromagnets. Adv. Funct. Mater. 2019, 29, 1901420. https://doi.org/10.1002/adfm.201901420. Impact Factor: 15.62
  9. Rodriguez, I. F., Megret, R., Acuna, E., Agosto-Rivera, J. L., & Giray, T. (2018). Recognition of Pollen-Bearing Bees from Video Using Convolutional Neural Network. Proceedings – 2018 IEEE Winter Conference on Applications of Computer Vision, WACV 2018, 2018-January, 314–322. https://doi.org/10.1109/WACV.2018.00041. Impact Factor: 3.55

20 Publications supported by HPCf (no acknowledgment)

  1. Pérez Claudio E, Rodriguez-Cruz Y, Arslan OC, Giray T, Agosto Rivera JL, Kence M, Wells H, Abramson CI. Appetitive reversal learning differences of two honey bee subspecies with different foraging behaviors. PeerJ. 2018 Nov 21;6:e5918. doi: 10.7717/peerj.5918. eCollection 2018. PubMed PMID: 30498631; PubMed Central
    PMCID: PMC6252072
  2. Ana M. Chicas-Mosier, Christopher W. Dinges, Jose L. Agosto-Rivera, Tugrul Giray, Devrim Oskay, Charles I. Abramson. Honey bees (Apis mellifera spp.) respond to increased aluminum exposure in their foraging choice, motility, and circadian rhythmicity. PLoS One. 2019; 14(6): e0218365. Published online 2019 Jun 27. doi: 10.1371/journal.pone.0218365 PMCID: PMC6597069
  3. Vega-Bellido GI, DeLaCruz-Araujo RA, Kretzschmar I, Córdova-Figueroa UM. Self-assembly of magnetic colloids with shifted dipoles. Soft Matter. 2019 May 22;15(20):4078-4086. doi: 10.1039/c8sm02591f. PubMed PMID: 30942785
  4. JianLvab, MeilingXua, ShiruLineXuecheng, ShaoaXinyuZhanga, YanhuiLiud, YanchaoWanga, ZhongfangChene, YanmingMaac. 2018. Direct-gap semiconducting tri-layer silicene with 29% photovoltaic efficiency. Science Direct. Nano Energy Volume 51, September 2018, Pages 489-495
  5. Li F, Chen Z. Cu dimer anchored on C(2)N monolayer: low-cost and efficient Bi-atom catalyst for CO oxidation. Nanoscale. 2018 Aug 23;10(33):15696-15705. doi: 10.1039/c8nr03394c. PubMed PMID: 30091768.
  6. Josell Ramirez-Paz, Manoj Saxena, Louis J. Delinois, Freisa M. Joaquín-Ovalle, Shiru Lin, Zhongfang Chen, Virginia A. Rojas-Nieves, Kai Griebenow. Site-specific PEGylation crosslinking of L-asparaginase subunits to improve its therapeutic efficiencybioRxiv 317040; doi: https://doi.org/10.1101/317040
  7. Fengyu Li, Fuzhao Yi, Junfeng Gao, Haijun Zhang, and Zhongfang Chen, Modulating the electronic properties of perovskite via σ–π interfacial interactions: A computational study. APL Materials 6, 114203 (2018); https://doi.org/10.1063/1.5044453
  8. Ya Wang,abc Jeffrey Comer, Zhongfang Chen, Jingwen Chen and James C. Gumbart, Exploring adsorption of neutral aromatic pollutants onto graphene nanomaterials via molecular dynamics simulations and theoretical linear solvation energy relationships. Environ. Sci.: Nano, 2018,5, 2117-2128
  9. Jia ZhaoJingxiang Zhao, Fengyu LiZhongfang Chen, Copper Dimer Supported on a C2N Layer as an Efficient Electrocatalyst for CO2 Reduction Reaction: A Computational Study. 2018. J. Phys. Chem. C20181223419712-19721
  10. C.-X. Liu, W.-H. Zhang, N. Wang, P. Guo, M. Muhler, Y. Wang, S. Lin, Z. Chen, G. Yang, Highly Efficient Photocatalytic Degradation of Dyes by a Copper–Triazolate Metal–Organic Framework. Chem. Eur. J. 2018, 24, 16804. PMID: 30133022.
  11. Lv X, Li F, Gong J, Chen Z. The dimensional and hydrogenating effect on the electronic properties of ZnSe nanomaterials: a computational investigation. Phys Chem Chem Phys. 2018 Oct 7;20(37):24453-24464. doi: 10.1039/c8cp04472d. Epub 2018 Sep 17. PubMed PMID: 30221293.
  12. Qiao M, Liu J, Wang Y, Li Y, Chen Z. PdSeO(3) Monolayer: Promising Inorganic 2D Photocatalyst for Direct Overall Water Splitting Without Using Sacrificial Reagents and Cocatalysts. J Am Chem Soc. 2018 Sep 26;140(38):12256-12262. doi: 10.1021/jacs.8b07855. Epub 2018 Sep 12. PubMed PMID: 30169028
  13. Chen W, Liu Z, Zhao Y, Yi X, Chen Z, Zheng A. To Be or Not To Be Protonated:cyclo-N(5)(-) in Crystal and Solvent. J Phys Chem Lett. 2018 Dec 20;9(24):7137-7145. doi: 10.1021/acs.jpclett.8b02841. Epub 2018 Dec 13. PubMed PMID: 30395479.
  14. Chen, Z., Zhao, J., Cabrera, C. R., Chen, Z., Computational Screening of Efficient Single‐Atom Catalysts Based on Graphitic Carbon Nitride (g‐C3N4) for Nitrogen Electroreduction.Small Methods 2019, 3, 1800368. https://doi.org/10.1002/smtd.201800368
  15. Zhe Chen, Jingxiang Zhao,Lichang Yin and Zhongfang Chen. 2019.B-terminated (111) polar surfaces of BP and BAs: promising metal-free electrocatalysts with large reaction regions for nitrogen fixation. J. Mater. Chem. A, 2019,7, 13284-13292
  16. Chunmei Zhang, Tianwei He, Sri Kasi Matta, Ting Liao, Liangzhi Kou, Zhongfang Chen, and Aijun Du. Predicting Novel 2D MB2 (M = Ti, Hf, V, Nb, Ta) Monolayers with Ultrafast Dirac Transport Channel and Electron-Orbital Controlled Negative Poisson’s Ratio The Journal of Physical Chemistry Letters 2019 10 (10), 2567-2573. DOI: 10.1021/acs.jpclett.9b00762
  17. Jun Long, Jinxing Gu, Zhanhong Yang, Jianfeng Mao,b Junnan Hao, Zhongfang Chen and Zaiping Guo. 2019. Highly porous, low band-gap NixMn3−xO4 (0.55 ≤ x ≤ 1.2) spinel nanoparticles with in situ coated carbon as advanced cathode materials for zinc-ion batteries. J. Mater. Chem. A, 2019,7, 17854-17866
  18. Benjamin, D. J., Berger, J. O., Johannesson, M., Nosek, B. A., Wagenmakers, E. J., Berk, R., … Johnson, V. E. (2018). Redefine statistical significance. Nature Human Behaviour, 2(1), 6-10. https://doi.org/10.1038/s41562-017-0189-z
  19. Jiménez, R. , Thurner, S. , Pericchi, L. R. and Klimek, P. (2019). Fraud Detection, Electoral. In Wiley StatsRef: Statistics Reference Online (eds N. Balakrishnan, T. Colton, B. Everitt, W. Piegorsch, F. Ruggeri and J. L. Teugels). doi:10.1002/9781118445112.stat08006
  20. M. J. Bayarri, James O. Berger, Woncheol Jang, Surajit Ray, Luis R. Pericchi & Ingmar Visser (2019) Prior-based Bayesian information criterion, Statistical Theory and Related Fields, 3:1, 2-13, DOI: 10.1080/24754269.2019.1582126

6 In press or Submitted that acknowledge HPCf or INBRE

  1. Electron confinement and magnetism of (LaTiO3)1/(SrTiO3)5 heterostructure: A diffusion quantum Monte Carlo study, , J. A. Santana,J. T. Krogel, S. Okamoto, and F. A. Reboredo1, J. Chem. Theory Comput. (2019)
  2. DFT calculations of the electrochemical adsorption of sulfuric acid anions on the Pt(110) and Pt(100) surfaces, J. A. Santana and Y. Ishikawa, J. Phys. Chem. C, (2019)
  3. Linear correlation models for the redox potential of organic molecules in aqueous solutions, J. C. Ortiz-Rodríguez, J. A. Santana and D. D. Méndez-Hernández, J. Molecular Modeling, (2019)
  4. Dieunel Derilus, Zillur Rahman, Fernando Pinero, and Steven Massey. The Black Queen, the Proteomic Constraint, and the dynamics of genome reduction in the photosynthetic picoeukaryotes. Applied and Environmental microbiology (AEM01616-19 )
  5. Dieunel Derilus , Filipa Godoy-Vitorino, Hebe Rosado Rivera, Edgardo Agosto, Maria Gloria Dominguez Bello , Humberto Cavallin. Unraveling the bacterial microcosms of a C-section operating room. Journal: PLOS Biology
  6. Oxygen Evolution Reaction on 2D Ferromagnetic Fe3GeTe2: Boosting the Reactivity by the Self-Reduction of Surface Hydroxy Yinghe Zhao, Jinxing Gu, and Zhongfang Chen*

01 May

HPCf Helpdesk Unscheduled Downtime and Alternative Contact

The HPCf Helpdesk is experiencing unexpected downtime. We are currently hard at work at fixing the issue, but until everything has been resolved, we will not be able to check the email address help@hpcf.upr.edu for incoming requests. Until maintenance work has finished, please direct any and all questions, requests, comments, or issues to the new, temporary address help.temp@hpcf.upr.edu. We are sorry for the inconvenience, and we thank you for  your patience and continued support of the HPCf.

11 Oct

Status Report After Hurricane Maria

We hope that this message finds you all safely.

As you all probably know, hurricane Maria has brought an unprecedented amount of devastation to all of Puerto Rico. The HPCf has luckily not suffered many damages and our staff and equipment are safe. Yesterday, 20 days after Maria’s passage through the island, we finally managed to restore most of our virtual machines, which host a significant amount of HPCf services, including our website.

At the time of writing, our cluster Boqueron seems to be working as usual, and users should be able to log in and submit jobs. During the hurricane, there was a power outage that knocked out 20 of Boqueron’s nodes and wiped out any jobs that were running there. Out of those 20 nodes, 19 have been restored. If you encounter any issues with Boqueron, please let us know.

While our machines are working close to normal, the HPCf offices themselves are still not fully operational. We have no electricity there yet, and so HPCf staff may be slow to respond to user tickets and inquiries. We thank you for your understanding during this difficult time.

We hope that you are all safe and that we can all recover quickly from hurricane Maria’s devastation.

18 Sep

HPCf Services During Hurricane Maria

As you all probably know, hurricane Maria is, at the time of writing, set to impact Puerto Rico starting this Wednesday as a category 4 hurricane. We are writing this post to explain what to expect from HPCf services during this time. In short, HPCf services will operate just like they did during hurricane Irma.

The HPCf machines are currently hosted at a private data center outside of any UPR campus or property. Our systems should be protected during the hurricane, and HPCf services (including jobs running on Boqueron) should continue to run as usual. If you manage to get electricity and an Internet connection (or if you are currently outside of Puerto Rico), you could, in theory, continue to work with HPCf resources even during the hurricane and its immediate aftermath.

That said, HPCf staff will not be available to provide regular support or maintenance to HPCf resources during the hurricane. That means that any help tickets will, unfortunately, remain unanswered until hurricane Maria has safely moved away from Puerto Rico. How quickly HPCf staff will be able to respond to support tickets during the aftermath of Maria will largely depend on the damage that Maria causes nationwide.

We are optimistic that our computers will not suffer downtime during the hurricane, but please keep in mind that it is still always a possibility that an outage could occur at the data center, and that such an outage could have unpredictable impact on user data. If you currently have absolutely crucial data on HPCf systems that you have not yet backed up–data that you absolutely cannot afford to lose–please make time during your hurricane preparations to back up your data. As stated in our Storage Policy, we do our best to protect user data, but users are ultimately responsible for keeping their data safe.

We appreciate your understanding, and we wish that you all stay safe during this major weather event.

05 Sep

HPCf Services During Hurricane Irma

As you all know, hurricane Irma is, at the time of writing, set to impact Puerto Rico starting tomorrow as a category 5 hurricane. We are writing this post to explain what to expect from HPCf services during this time.

The HPCf machines are currently hosted at a private data center outside of any UPR campus or property. Our systems should be protected during the hurricane, and HPCf services (including jobs running on Boqueron) should continue to run as usual. If you manage to get electricity and an Internet connection (or if you are currently outside of Puerto Rico), you could, in theory, continue to work with HPCf resources even during the hurricane and its immediate aftermath.

That said, HPCf staff will not be available to provide regular support or maintenance to HPCf resources during the hurricane. That means that any help tickets will, unfortunately, remain unanswered until hurricane Irma has safely moved away from Puerto Rico. How quickly HPCf staff will be able to respond to support tickets during the aftermath of Irma will largely depend on the damage that Irma causes nationwide.

We are optimistic that our computers will not suffer downtime during the hurricane, but please keep in mind that it is still always a possibility that an outage could occur at the data center, and that such an outage could have unpredictable impact on user data. If you currently have absolutely crucial data on HPCf systems that you have not yet backed up–data that you absolutely cannot afford to lose–please make time during your hurricane preparations to back up your data. As stated in our Storage Policy, we do our best to protect user data, but users are ultimately responsible for keeping their data safe.

We appreciate your understanding, and we wish that you all stay safe during this unprecedented weather event.

 

19 Jun

Old Cluster Nanobio’s Retirement

We at the HPCf have decided that our old cluster Nanobio (Boqueron’s predecessor) will be retired after the end of July of this year. On August 1st, 2017, Nanobio will be powered down and any data left in any of its file systems (including /home and /work) will no longer be available from that time onward. As we have done since Boqueron went online on March 2016, we encourage all users who still have any data on Nanobio to move or copy it to some other system as soon as possible. Transferring data to Boqueron is one option, but please keep in mind that, per our usage policies, users should transfer to Boqueron only the data that they will actually need for their work there; Boqueron is not designed or intended for long-term storage. Users will be responsible for making sure they do not incur any data loss as a result of Nanobio’s retirement.

Any users whose HPCf accounts were created after Boqueron went online may disregard this notice since they do not have a Nanobio account. As always, if you have any questions or comments, feel free to send them to help@hpcf.upr.edu.

26 Jan

Boqueron Scheduled Partial Downtime Jan 30 – Jan 31, 2017

The staff from the data center where Boqueron is hosted at will be carrying out some electrical work next week that will impact Boqueron.  To cooperate with the efforts and to protect as many jobs as possible from getting spontaneously killed, we have opened a maintenance window starting at 7:30am Monday January 30th and ending at 12:00pm Tuesday January 31st.   Any newly submitted jobs that cannot complete before the maintenance window begins will be held in the queue until the window ends.

During this window, the Boqueron login node will continue to operate, and the file systems /home and /work should continue to be available, so you should be able to access your files during this time.  The worker nodes will be powered down, however.

Jobs that are currently running will be allowed to continue to run, but if any remain running at the time of the maintenance window, they will unfortunately be killed.

We realize this announcement comes a bit short notice, but please understand that HPCf staff was notified of this electrical work yesterday afternoon.

We apologize for any inconvenience you may experience from this maintenance window, and we thank you for your cooperation.  As always, if you have any questions or comments, please send them to help@hpcf.upr.edu.

31 Oct

Boqueron Power Outage During the Halloween Weekend

An unexpected outage in the data center where Boqueron is hosted wiped out 60 of Boqueron’s nodes over the weekend. All jobs running on those nodes were killed.  We have since turned the nodes back on and they should now be working as usual.

To make sure the entire cluster has recovered from the outage, the 20 nodes that remained up during the outage (nodes 41~60) will be rebooted at a later time, and so they will remain closed off to new jobs until then (they will be listed as either “draining” or “drained” by Slurm). The jobs that are currently running there will be allowed to run uninterrupted.

The outage did not affect Boqueron’s login node or Boqueron’s /home or /work file systems.  Other HPCf services such as our web site, however, were affected.  They are also back online, and you should not experience any issues when using them.

We are currently in talks with the administrators at the data center to asses the situation and prevent it from occurring again.

As always, if you have any questions, problems, or comment, you may write to us at help@hpcf.upr.edu.

15 Aug

/work Filesystem Outtage Has Been Fixed

Early today, Boqueron’s /work had a hiccup and it went offline for a few hours.  This caused some weird behavior, including not being able to sign in through certain software such as SCP programs.  We’ve fixed the issue, but because jobs run on /work, the running jobs that remained after /work went offline eventually got killed.  Everything should be fine now and you should be able to resubmit your jobs with no problems.  No data loss should have occurred as a result of this error.

Please remember that per HPCf Usage Policies, data in /work is not backed up.  Always make sure to move important data off of /work and into a more permanent storage location, such as a computer in your laboratory or a personal workstation.

As always, if you have any other issues or questions, please let us know at help@hpcf.upr.edu.

01 Jun

Boqueron Unscheduled Maintenance During Morning of June 1st, 2016

As you may have noticed, Boqueron underwent unscheduled, urgent maintenance earlier today.  This maintenance unfortunately had the effect of killing all running and pending jobs in the process.

What happened?

An issue in the way Slurm (the queue manager) was interacting with the cluster manager software that we use on Boqueron (Bright CM) was causing Slurm’s configuration to get rewritten spontaneously when certain actions were taken in the cluster.  Every time this happened, jobs got killed.  Today, we contacted Bright support and they were kind enough to help us out through a live screen-sharing session.  The changes they had to make required the Slurm configuration to get rewritten much like those other times, and so earlier today jobs got killed as well.

Is the issue resolved?

Yes.  The issue was bugging us for a few weeks now, but it should now be completely resolved.

Can I submit jobs again?  Won’t they get killed again?

Yes, you may submit jobs again; and no, they should not get killed again.  No system is perfect, but the solution we arrived at today with Bright support should result in continuous, stable queue operation under normal, day-to-day circumstances.

But I’m afraid they’ll get killed again!

You shouldn’t be afraid.  We recognize that the recent shakiness of the queues would cause user confidence to drop, but again, the core issue should now be resolved and we expect stable times for our cluster. *knocks on wood*

We do apologize for the inconvenience this has created.  For any further questions or comments, feel free to contact us at help@hpcf.upr.edu.