22 Jun

Boqueron Back Online – June 22, 2020

Boqueron’s replacement switch has finally been installed and Boqueron is back online. Users should be able to log back in and use the cluster normally.

Before resuming your work, we invite you to take a few moments to back up all your data currently on Boqueron. Please remember that, per our Storage Policy:

Boqueron is not meant to provide reliable long-term storage. We do our best to keep users’ data safe, but by making use of the HPCf cluster (and HPCf systems in general), users agree that they are the ones ultimately responsible for keeping their own data safe, including keeping their own backups outside of HPCf systems.

We thank you for your patience during this outage and we apologize for the impact it no doubt had on your work. As always, please send any questions or comments to help@hpcf.upr.edu, and we will gladly get back to you.

03 Jun

Boqueron Unplanned Downtime Status Report – June 3, 2020

The purchase of the replacement switch for Boqueron is underway. Due to the pandemic, it is difficult to estimate how long it’ll actually take for the switch to ship and arrive to us, but we wanted to let our users know how things are proceeding.

We will most likely have to wait for the switch to arrive in order to reestablish user access to their data, since the alternatives that we considered do not seem viable.

We will continue updating on Boqueron’s status as new developments occur. As always, feel free to write any questions or comments to help@hpcf.upr.edu, and we will get back to you as soon possible.

26 May

Boqueron Unplanned Downtime Status Report – May 26, 2020

During the past week we identified the main issue that has caused the downtime and we began taking steps to resolve it. The problem lies in Boqueron’s main internal 10 G switch, which, after extensive testing, we have concluded will unfortunately need to be replaced. We have begun the process of obtaining quotes for the new switch to proceed with a purchase.

We are also discussing what our alternatives are during the time it will take for the replacement switch to arrive. We will update as soon as we have a decision regarding this matter.

We would like to at least restore user access to their files as soon as possible, but this too is impacted by the network outage: the /home directory is located in one machine, but the LDAP server (similar to a Windows Active Directory) used to authenticate users (so they can log in) is in a separate computer (this is by design; it is not an error), and without a means of getting the two machines to talk to each other, users will not be able to log in to their files.

We apologize for the inconvenience this outage has no doubt caused to your work. As always, please send any questions or comments to help@hpcf.upr.edu and we will get back to you as soon as possible.

19 May

Boqueron Unplanned Downtime – May 19, 2020

An internal networking issue is disrupting Boqueron’s operations. User data is safe, but it is currently inaccessible to users until the issue is resolved. We are working both remotely and on-site to fix the issue as quickly as possible within the restrictions in place to stop the spread of the coronavirus. We will update with more details as they become available.

As always, if you have any questions or comments, feel free to write to us at help@hpcf.upr.edu.

12 Feb

Boqueron Back Online at Reduced Capacity

This is a quick note to let our users know that the maintenance work scheduled for today Wednesday, February 12 went as planned and Boqueron is back online at reduced capacity.

As indicated in this week’s earlier post, Boqueron will continue to operate at reduced capacity until the electrical work at the data center is completed.

As always, if you have any questions or comments, please send them to help@hpcf.upr.edu.

10 Feb

Boqueron Planned Maintenance This Week

The data center where the Boqueron cluster is hosted will be undergoing some electrical maintenance from Saturday, February 15 to Sunday, February 16. The electrical work will require a full power down of Boqueron this Wednesday, February 12. After Boqueron is brought back online (which should happen the same day), it will operate at reduced capacity until the electrical work at the data center is completed. “Reduced capacity” means that a significant portion of Boqueron’s nodes will remain offline in order to lighten the load on the the data center’s circuits.

Because of this, we have placed some limits on the jobs Boqueron may currently accept. Specifically, any jobs that cannot complete their run by 8:00 am Wednesday will not be accepted until Boqueron is powered down and brought back online. Furthermore, once Boqueron is brought back online, only half of its nodes will be available to run jobs, so the remaining half will not accept any jobs until the electrical maintenance is completed at the data center.

All of Boqueron’s nodes will be powered down on Wednesday morning. Any jobs currently running will continue as usual, but, if they are still running by the time the nodes are powered down, they will unfortunately be killed.

We realize this information comes on a somewhat short notice, but we at the HPCf were only informed recently that the date for the electrical work would be this weekend, so we had no way of alerting our users much earlier than this. We apologize for any inconvenience this situation may cause for your work.

Half of Boqueron’s node are set to be powered back on on Wednesday, February 12. The rest are set to be powered up again on Monday, February 17. The nodes that will remain powered off throughout the weekend are the following: node011 through node020, node031 through node040, node051 through node060, and node071 through node080.

As always, if you have any questions or comments, please send them to help@hpcf.upr.edu.

20 Nov

Boqueron Decreased Capacity During the Weekend

The data center where the Boqueron cluster is hosted will be undergoing some electrical maintenance from Saturday November 23 to Sunday November 24. The electrical work requires that we power down a significant portion of Boqueron’s nodes in order to lighten the load on the the data center’s circuits.

Because of this, we have decided to stop accepting new jobs on half of Boqueron’s nodes effective immediately. These “drained” nodes will be powered down on Friday morning. Any jobs currently running on these nodes will continue as usual, but, if they are still running by the time the nodes are powered down, they will unfortunately be killed.

We realize this information comes on a somewhat short notice, but we at the HPCf were only informed today that the date for the electrical work would be this weekend, so we had no way of alerting our users earlier. We apologize for any inconvenience this situation may cause for your work.

All the affected nodes will be powered on again on Monday November 25. The nodes affected by this maintenance are the following: node011 through node020, node031 through node040, node051 through node060, and node071 through node080.

As always, if you have any questions or comments, please send them to help@hpcf.upr.edu.

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.