May 2015 - Allocations-admins - mailman3.cels.anl.gov

Re: [allocations-admins] [LCRC Accounts] Project Request: Irridates
by Bair, Raymond A. 28 May '15

28 May '15

After further thought, I propose that we grant this request as it stands. I will then let Peter know that Fusion might be more available than Blues. It is not a large enough project to make much of a point about shifting off Blues. Ray ----------------------------------------- Ray Bair Computing, Environment, and Life Sciences Argonne National Laboratory and the University of Chicago TCS Building 240, Room 4122 9700 South Cass Avenue Argonne, IL 60439 email: rbair(at)anl.gov Phone: (630)252-5751 On 5/26/15, 4:25 PM, "accounts(a)lcrc.anl.gov" <accounts(a)lcrc.anl.gov> wrote: >Hello, > >A new project on the LCRC cluster has been requested. Please forward >the information on to the LCRC Allocation sub-committee. > > Applicant's name: Peter Littlewood >Applicant's institution: ANL > Applicant's division: PSE > Project Name: Irridates > Project title: Metal-insulator phase transitions in irridates > Associated funding: DoE > Other Systems: > Science: Our goal is to investigate the role of the rare >earth elements (R) in metal-insulator transitions >of pyrochlore irridate compounds. Contrary to what >expected, the R-dependence in a single-site DMFT >calculation with local Coulomb interaction is >very weak. We want to perform cluster DMFT calculations for three >irridate compounds (Lu, Y, and Eu) with configuration-interaction-based >exact diagonalization solvers. > Project description: We will use MPI Fortran codes developed at >Coulumbia University at NYC. Based on previous >cluster DMFT calculations for a model tight >binding Hamiltonian we estimate the CPU hours for >a submitted job as 10k: 12 nodes * 16 cores per >node (Blues) running for 48 hours. >The work will be divided in multiple sets >containing external parameters. Considering the >limited resources, we will target parameters to >solve instead of surveying entire phase diagram. >Previous tests using thousands of cores >simultaneously indicate that a better performance >is achieved running jobs on hundreds of cores. >The project is expected to have three members at >most. > Industry partnership: > Project URL: > Requested allocation: 350000 > Q1: 0 > Q2: 0 > Q3: 0 > Q4: 350000 > Justification: > Storage requirements: less that 1 TB > > >The requester has used undetermined amount hours of their initial startup >project. > >In addition to approving an initial amount, please specify a Category >and Subcategory for this project. For a list of the current selection >of approved categories, please see: > > https://wiki.lcrc.anl.gov/wiki/Processes/Categories > >Once the Allocation committee has approved the project, please go to >the Project Management page to create it: > >https://accounts.lcrc.anl.gov/projects.php > >Thank You, >The LCRC Accounts System >_______________________________________________ >allocations-admins mailing list >allocations-admins(a)lcrc.anl.gov >https://lists.lcrc.anl.gov/mailman/listinfo/allocations-admins

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Re: [allocations-admins] [LCRC Accounts] Project Allocation Request
by John Blaas 27 May '15

27 May '15

Allocation for 200k core hours has been granted. - JB On Tue, May 26, 2015 at 10:46 AM, accounts(a)lcrc.anl.gov <accounts(a)lcrc.anl.gov> wrote: > Hello, > > A change in allocation has been requested: > > Requester: ellisrj (Ross Ellis) > Project: DMDOHEMA_1 > Title: Metal Ion Transport through Nano-Structured Lipophilic Systems: Atomistic MD Simulations > Description: In the last few months, we have performed some preliminary simulation runs in understanding the supra-molecular aggregate structure in organic phases under the project DMDOHEMA_1 on LCRC. Some findings have been unveiled, e.g., the presences of water, acid, Eu(NO3)3 all affect the supra-molecular aggregate structure of extractant (i.e., DMDOHEMA) in organic phased. These findings agree with the existing experimental data. However, due to the small size of those simulation systems, the aggregation behaviors are not converged well. Therefore, in the renewal period of project DMDOHEMA_1, we are aiming to enlarge our simulation boxes so that such findings can be solidified. Moreover, one already finished large simulation supports that larger simulation box decreases the calculated error bar of the aggregation number of DMDOHEMA. With the simulations on large enough simulation boxes, the effects of water, acid, Eu(NO3)3 will be distinguished, which will surely provi > de significant insight for the rational design of higher efficient extractants. Our project is expected to highly spark the development of rare earth element related technologies. > In this project, classical molecular dynamics (MD) simulations will be performed at the all-atom resolution, in addition to the concurrent solvent extraction experiments at ANL. All-atom MD simulations have been well proven in predicting supra-molecular aggregate structures. The open source package GROMACS will be employed for the simulations. GROMACS is one of the highly recommended packages for MD simulations. GROMACS has been reported to be able to scale well up to around 1,000 CPU processors. Based on our experience on LCRC, the simulations can be LINEARLY scaled up to 256 CPU cores, under which condition the simulation speed is around 3 hours/ns for a system of the size of around 17 Ã— 17 Ã— 17 = 5000 nm3. > Two users will use this allocation time, Dr. Ross J. Ellis and Dr. Baofu Qiao, both at the CSE division at ANL. > In the first phase of this project, we are studying the influence of a variety of components, i.e., water, acid, Eu(NO3)3, on the aggregate structures of DMDOHEMA extractants dissolved in n-heptane organic phases. As aforementioned, this project is currently ongoing. With the allocation from LCRC, we are able to collects some conclusions in the near fure. > In the second phase, we plan to study the effect of extractant on the supra-molecula aggregate structure. The extraction of DMDBTDMA, which is the preceding extractant of DMDOHEMA, will be simulated and compared with the simulation results of DMDOHEMA systems. According to the available experimental data, the effects of some factors will be explore, such as the concentration of water, the concentration of Eu(NO3)3 complexes, the concentration of acidic molecule of HNO3. > > > > Current: undetermined amount > Justification: Table. Benchmark of the simulation speed on LCRC > #CPU cores 16 32 64 256 > Speed > (ns/day) 0.51 1.0 2.0 7.7 > > Based on the benchmark simulations, we can conclude that the scaling on LCRC can be linearly up to at least 256 CPU cores for our simulations. > > > Requested: 400000 > > A specific reason has been given: > We are currently using the AMBER molecular dynamics simulation package for polarizable simulations. We have observed some better agreements with experimental data using polarazable force field. Under AMBER, the program sander.MPI is used for the polarizable simulations. > Based on our tests, the optimal performance is obtained when using 6 node with 16 cores per node. See the following for the results. With these test results, a total amount of allocation of 400,000 core hours is requests. > > #node (ppn=16): 2 3 4 5 6 7 > 8 > speed (ns/day) : 0.56 0.83 0.78 1.14 1.33 1.39 0.99 > > > This needs to be approved and the final allocation amount decided upon. > > Thank You, > The LCRC Accounts System

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Re: [allocations-admins] [LCRC Accounts] Project Allocation Request
by Low, John J. 27 May '15

27 May '15

I assume so. The license fee for an individual is less. John J. Low Principal Computational Science Specialist Computing, Environment and Life Sciences Building 240, 2143 9700 South Cass Avenue Argonne National Laboratory Argonne, IL 60439. 630-252-0045 www.linkedin.com/pub/john-low/15/8b0/5aa/ -----Original Message----- From: <Bair>, "Bair, Raymond A." <rbair(a)anl.gov> Reply-To: LCRC Allocations Admins <allocations-admins(a)lcrc.anl.gov> Date: Wednesday, May 27, 2015 at 10:46 AM To: LCRC Allocations Admins <allocations-admins(a)lcrc.anl.gov> Subject: Re: [allocations-admins] [LCRC Accounts] Project Allocation Request >Did that project buy the license? > >----------------------------------------- >Ray Bair >Computing, Environment, and Life Sciences >Argonne National Laboratory > and the University of Chicago >TCS Building 240, Room 4122 >9700 South Cass Avenue >Argonne, IL 60439 >email: rbair(at)anl.gov >Phone: (630)252-5751 > > > > > >On 5/27/15, 9:03 AM, "Low, John J." <jlow(a)mcs.anl.gov> wrote: > >>Ray, >> >>Amber requires a $2000 license fee for computing centers in nonprofits. >> >> >>John J. Low >>Principal Computational Science Specialist >>Computing, Environment and Life Sciences >>Building 240, 2143 >>9700 South Cass Avenue >>Argonne National Laboratory >>Argonne, IL 60439. >>630-252-0045 >>www.linkedin.com/pub/john-low/15/8b0/5aa/ >> >> >>________________________________________ >>From: allocations-admins-bounces(a)lcrc.anl.gov >>[allocations-admins-bounces(a)lcrc.anl.gov] on behalf of Bair, Raymond A. >>[rbair(a)anl.gov] >>Sent: Wednesday, May 27, 2015 8:44 AM >>To: LCRC Allocations Admins >>Subject: Re: [allocations-admins] [LCRC Accounts] Project Allocation >>Request >> >>John, >> >>Did you see their comments about how the polarization model in Amber >>worked better for them? >> >> >> >>----------------------------------------- >>Ray Bair >>Computing, Environment, and Life Sciences >>Argonne National Laboratory >> and the University of Chicago >>TCS Building 240, Room 4122 >>9700 South Cass Avenue >>Argonne, IL 60439 >>email: rbair(at)anl.gov >>Phone: (630)252-5751 >> >> >> >> >> >>On 5/26/15, 4:31 PM, "Low, John J." <jlow(a)mcs.anl.gov> wrote: >> >>>Ray, >>> >>>The authors of GROMACS are claiming a 3-5 speedup on gpus over a 6-core >>>haswell desktop (like my home system). Ellis, et al. could use the gpu >>>nodes on Blues or Fusion nodes. These nodes don’t seem to be heavily >>>used. >>> >>>See http://www.gromacs.org/GPU_acceleration. >>> >>>The GROMACS GPU benchmarks show good performance for models containing >>>100,000 or more atoms. If he is planning to use a model of that size, >>>then he could benefit by using the GPUs. >>> >>>John J. Low >>>Principal Computational Science Specialist >>>Computing, Environment and Life Sciences >>>Building 240, 2143 >>>9700 South Cass Avenue >>>Argonne National Laboratory >>>Argonne, IL 60439. >>>630-252-0045 >>>www.linkedin.com/pub/john-low/15/8b0/5aa/ >>> >>> >>> >>> >>> >>> >>>-----Original Message----- >>>From: <Bair>, "Bair, Raymond A." <rbair(a)anl.gov> >>>Reply-To: LCRC Allocations Admins <allocations-admins(a)lcrc.anl.gov> >>>Date: Tuesday, May 26, 2015 at 10:58 AM >>>To: "Ellis, Ross J." <rellis(a)anl.gov> >>>Cc: LCRC Allocations Admins <allocations-admins(a)lcrc.anl.gov> >>>Subject: Re: [allocations-admins] [LCRC Accounts] Project Allocation >>>Request >>> >>>>Dear Ross, >>>> >>>>At this time Blues is very full, so we have been asking projects to >>>>move >>>>to Fusion when they request large amounts of additional time in FY2015. >>>>Can your team use Fusion (8 cores per node) to do the proposed >>>>calculations? >>>> >>>>Also, for this size of a request we will need to poll the LCRC >>>>Allocations >>>>Committee. FYI, Al Wagner is your point of contact on this committee. >>>> >>>>Regards, >>>> >>>>Ray >>>> >>>>----------------------------------------- >>>>Ray Bair >>>>Computing, Environment, and Life Sciences >>>>Argonne National Laboratory >>>> and the University of Chicago >>>>TCS Building 240, Room 4122 >>>>9700 South Cass Avenue >>>>Argonne, IL 60439 >>>>email: rbair(at)anl.gov >>>>Phone: (630)252-5751 >>>> >>>> >>>> >>>> >>>> >>>>On 5/26/15, 10:46 AM, "accounts(a)lcrc.anl.gov" <accounts(a)lcrc.anl.gov> >>>>wrote: >>>> >>>>>Hello, >>>>> >>>>>A change in allocation has been requested: >>>>> >>>>> Requester: ellisrj (Ross Ellis) >>>>> Project: DMDOHEMA_1 >>>>> Title: Metal Ion Transport through Nano-Structured Lipophilic >>>>>Systems: Atomistic MD Simulations >>>>> Description: In the last few months, we have performed some >>>>>preliminary >>>>>simulation runs in understanding the supra-molecular aggregate >>>>>structure >>>>>in organic phases under the project DMDOHEMA_1 on LCRC. Some findings >>>>>have been unveiled, e.g., the presences of water, acid, Eu(NO3)3 all >>>>>affect the supra-molecular aggregate structure of extractant (i.e., >>>>>DMDOHEMA) in organic phased. These findings agree with the existing >>>>>experimental data. However, due to the small size of those simulation >>>>>systems, the aggregation behaviors are not converged well. Therefore, >>>>>in >>>>>the renewal period of project DMDOHEMA_1, we are aiming to enlarge our >>>>>simulation boxes so that such findings can be solidified. Moreover, >>>>>one >>>>>already finished large simulation supports that larger simulation box >>>>>decreases the calculated error bar of the aggregation number of >>>>>DMDOHEMA. >>>>>With the simulations on large enough simulation boxes, the effects of >>>>>water, acid, Eu(NO3)3 will be distinguished, which will surely provi >>>>> de significant insight for the rational design of higher efficient >>>>>extractants. Our project is expected to highly spark the development >>>>>of >>>>>rare earth element related technologies. >>>>>In this project, classical molecular dynamics (MD) simulations will be >>>>>performed at the all-atom resolution, in addition to the concurrent >>>>>solvent extraction experiments at ANL. All-atom MD simulations have >>>>>been >>>>>well proven in predicting supra-molecular aggregate structures. The >>>>>open >>>>>source package GROMACS will be employed for the simulations. GROMACS >>>>>is >>>>>one of the highly recommended packages for MD simulations. GROMACS has >>>>>been reported to be able to scale well up to around 1,000 CPU >>>>>processors. >>>>>Based on our experience on LCRC, the simulations can be LINEARLY >>>>>scaled >>>>>up to 256 CPU cores, under which condition the simulation speed is >>>>>around >>>>>3 hours/ns for a system of the size of around 17 Ã‹ 17 Ã‹ 17 = 5000 >>>>>nm3. >>>>>Two users will use this allocation time, Dr. Ross J. Ellis and Dr. >>>>>Baofu >>>>>Qiao, both at the CSE division at ANL. >>>>>In the first phase of this project, we are studying the influence of a >>>>>variety of components, i.e., water, acid, Eu(NO3)3, on the aggregate >>>>>structures of DMDOHEMA extractants dissolved in n-heptane organic >>>>>phases. >>>>>As aforementioned, this project is currently ongoing. With the >>>>>allocation >>>>>from LCRC, we are able to collects some conclusions in the near fure. >>>>>In the second phase, we plan to study the effect of extractant on the >>>>>supra-molecula aggregate structure. The extraction of DMDBTDMA, which >>>>>is >>>>>the preceding extractant of DMDOHEMA, will be simulated and compared >>>>>with >>>>>the simulation results of DMDOHEMA systems. According to the available >>>>>experimental data, the effects of some factors will be explore, such >>>>>as >>>>>the concentration of water, the concentration of Eu(NO3)3 complexes, >>>>>the >>>>>concentration of acidic molecule of HNO3. >>>>> >>>>> >>>>> >>>>> Current: undetermined amount >>>>>Justification: Table. Benchmark of the simulation speed on LCRC >>>>>#CPU cores 16 32 64 256 >>>>>Speed >>>>>(ns/day) 0.51 1.0 2.0 7.7 >>>>> >>>>>Based on the benchmark simulations, we can conclude that the scaling >>>>>on >>>>>LCRC can be linearly up to at least 256 CPU cores for our simulations. >>>>> >>>>> >>>>> Requested: 400000 >>>>> >>>>>A specific reason has been given: >>>>>We are currently using the AMBER molecular dynamics simulation package >>>>>for polarizable simulations. We have observed some better agreements >>>>>with >>>>>experimental data using polarazable force field. Under AMBER, the >>>>>program >>>>>sander.MPI is used for the polarizable simulations. >>>>>Based on our tests, the optimal performance is obtained when using 6 >>>>>node >>>>>with 16 cores per node. See the following for the results. With these >>>>>test results, a total amount of allocation of 400,000 core hours is >>>>>requests. >>>>> >>>>>#node (ppn=16): 2 3 4 5 6 7 >>>>> 8 >>>>>speed (ns/day) : 0.56 0.83 0.78 1.14 1.33 1.39 0.99 >>>>> >>>>> >>>>>This needs to be approved and the final allocation amount decided >>>>>upon. >>>>> >>>>>Thank You, >>>>>The LCRC Accounts System >>>> >>>>_______________________________________________ >>>>allocations-admins mailing list >>>>allocations-admins(a)lcrc.anl.gov >>>>https://lists.lcrc.anl.gov/mailman/listinfo/allocations-admins >>> >>>_______________________________________________ >>>allocations-admins mailing list >>>allocations-admins(a)lcrc.anl.gov >>>https://lists.lcrc.anl.gov/mailman/listinfo/allocations-admins >> >>_______________________________________________ >>allocations-admins mailing list >>allocations-admins(a)lcrc.anl.gov >>https://lists.lcrc.anl.gov/mailman/listinfo/allocations-admins >>_______________________________________________ >>allocations-admins mailing list >>allocations-admins(a)lcrc.anl.gov >>https://lists.lcrc.anl.gov/mailman/listinfo/allocations-admins > >_______________________________________________ >allocations-admins mailing list >allocations-admins(a)lcrc.anl.gov >https://lists.lcrc.anl.gov/mailman/listinfo/allocations-admins

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Re: [allocations-admins] [LCRC Accounts] Project Allocation Request
by Bair, Raymond A. 27 May '15

27 May '15

Did that project buy the license? ----------------------------------------- Ray Bair Computing, Environment, and Life Sciences Argonne National Laboratory and the University of Chicago TCS Building 240, Room 4122 9700 South Cass Avenue Argonne, IL 60439 email: rbair(at)anl.gov Phone: (630)252-5751 On 5/27/15, 9:03 AM, "Low, John J." <jlow(a)mcs.anl.gov> wrote: >Ray, > >Amber requires a $2000 license fee for computing centers in nonprofits. > > >John J. Low >Principal Computational Science Specialist >Computing, Environment and Life Sciences >Building 240, 2143 >9700 South Cass Avenue >Argonne National Laboratory >Argonne, IL 60439. >630-252-0045 >www.linkedin.com/pub/john-low/15/8b0/5aa/ > > >________________________________________ >From: allocations-admins-bounces(a)lcrc.anl.gov >[allocations-admins-bounces(a)lcrc.anl.gov] on behalf of Bair, Raymond A. >[rbair(a)anl.gov] >Sent: Wednesday, May 27, 2015 8:44 AM >To: LCRC Allocations Admins >Subject: Re: [allocations-admins] [LCRC Accounts] Project Allocation >Request > >John, > >Did you see their comments about how the polarization model in Amber >worked better for them? > > > >----------------------------------------- >Ray Bair >Computing, Environment, and Life Sciences >Argonne National Laboratory > and the University of Chicago >TCS Building 240, Room 4122 >9700 South Cass Avenue >Argonne, IL 60439 >email: rbair(at)anl.gov >Phone: (630)252-5751 > > > > > >On 5/26/15, 4:31 PM, "Low, John J." <jlow(a)mcs.anl.gov> wrote: > >>Ray, >> >>The authors of GROMACS are claiming a 3-5 speedup on gpus over a 6-core >>haswell desktop (like my home system). Ellis, et al. could use the gpu >>nodes on Blues or Fusion nodes. These nodes don’t seem to be heavily >>used. >> >>See http://www.gromacs.org/GPU_acceleration. >> >>The GROMACS GPU benchmarks show good performance for models containing >>100,000 or more atoms. If he is planning to use a model of that size, >>then he could benefit by using the GPUs. >> >>John J. Low >>Principal Computational Science Specialist >>Computing, Environment and Life Sciences >>Building 240, 2143 >>9700 South Cass Avenue >>Argonne National Laboratory >>Argonne, IL 60439. >>630-252-0045 >>www.linkedin.com/pub/john-low/15/8b0/5aa/ >> >> >> >> >> >> >>-----Original Message----- >>From: <Bair>, "Bair, Raymond A." <rbair(a)anl.gov> >>Reply-To: LCRC Allocations Admins <allocations-admins(a)lcrc.anl.gov> >>Date: Tuesday, May 26, 2015 at 10:58 AM >>To: "Ellis, Ross J." <rellis(a)anl.gov> >>Cc: LCRC Allocations Admins <allocations-admins(a)lcrc.anl.gov> >>Subject: Re: [allocations-admins] [LCRC Accounts] Project Allocation >>Request >> >>>Dear Ross, >>> >>>At this time Blues is very full, so we have been asking projects to move >>>to Fusion when they request large amounts of additional time in FY2015. >>>Can your team use Fusion (8 cores per node) to do the proposed >>>calculations? >>> >>>Also, for this size of a request we will need to poll the LCRC >>>Allocations >>>Committee. FYI, Al Wagner is your point of contact on this committee. >>> >>>Regards, >>> >>>Ray >>> >>>----------------------------------------- >>>Ray Bair >>>Computing, Environment, and Life Sciences >>>Argonne National Laboratory >>> and the University of Chicago >>>TCS Building 240, Room 4122 >>>9700 South Cass Avenue >>>Argonne, IL 60439 >>>email: rbair(at)anl.gov >>>Phone: (630)252-5751 >>> >>> >>> >>> >>> >>>On 5/26/15, 10:46 AM, "accounts(a)lcrc.anl.gov" <accounts(a)lcrc.anl.gov> >>>wrote: >>> >>>>Hello, >>>> >>>>A change in allocation has been requested: >>>> >>>> Requester: ellisrj (Ross Ellis) >>>> Project: DMDOHEMA_1 >>>> Title: Metal Ion Transport through Nano-Structured Lipophilic >>>>Systems: Atomistic MD Simulations >>>> Description: In the last few months, we have performed some >>>>preliminary >>>>simulation runs in understanding the supra-molecular aggregate >>>>structure >>>>in organic phases under the project DMDOHEMA_1 on LCRC. Some findings >>>>have been unveiled, e.g., the presences of water, acid, Eu(NO3)3 all >>>>affect the supra-molecular aggregate structure of extractant (i.e., >>>>DMDOHEMA) in organic phased. These findings agree with the existing >>>>experimental data. However, due to the small size of those simulation >>>>systems, the aggregation behaviors are not converged well. Therefore, >>>>in >>>>the renewal period of project DMDOHEMA_1, we are aiming to enlarge our >>>>simulation boxes so that such findings can be solidified. Moreover, one >>>>already finished large simulation supports that larger simulation box >>>>decreases the calculated error bar of the aggregation number of >>>>DMDOHEMA. >>>>With the simulations on large enough simulation boxes, the effects of >>>>water, acid, Eu(NO3)3 will be distinguished, which will surely provi >>>> de significant insight for the rational design of higher efficient >>>>extractants. Our project is expected to highly spark the development of >>>>rare earth element related technologies. >>>>In this project, classical molecular dynamics (MD) simulations will be >>>>performed at the all-atom resolution, in addition to the concurrent >>>>solvent extraction experiments at ANL. All-atom MD simulations have >>>>been >>>>well proven in predicting supra-molecular aggregate structures. The >>>>open >>>>source package GROMACS will be employed for the simulations. GROMACS is >>>>one of the highly recommended packages for MD simulations. GROMACS has >>>>been reported to be able to scale well up to around 1,000 CPU >>>>processors. >>>>Based on our experience on LCRC, the simulations can be LINEARLY scaled >>>>up to 256 CPU cores, under which condition the simulation speed is >>>>around >>>>3 hours/ns for a system of the size of around 17 Ã‹ 17 Ã‹ 17 = 5000 >>>>nm3. >>>>Two users will use this allocation time, Dr. Ross J. Ellis and Dr. >>>>Baofu >>>>Qiao, both at the CSE division at ANL. >>>>In the first phase of this project, we are studying the influence of a >>>>variety of components, i.e., water, acid, Eu(NO3)3, on the aggregate >>>>structures of DMDOHEMA extractants dissolved in n-heptane organic >>>>phases. >>>>As aforementioned, this project is currently ongoing. With the >>>>allocation >>>>from LCRC, we are able to collects some conclusions in the near fure. >>>>In the second phase, we plan to study the effect of extractant on the >>>>supra-molecula aggregate structure. The extraction of DMDBTDMA, which >>>>is >>>>the preceding extractant of DMDOHEMA, will be simulated and compared >>>>with >>>>the simulation results of DMDOHEMA systems. According to the available >>>>experimental data, the effects of some factors will be explore, such as >>>>the concentration of water, the concentration of Eu(NO3)3 complexes, >>>>the >>>>concentration of acidic molecule of HNO3. >>>> >>>> >>>> >>>> Current: undetermined amount >>>>Justification: Table. Benchmark of the simulation speed on LCRC >>>>#CPU cores 16 32 64 256 >>>>Speed >>>>(ns/day) 0.51 1.0 2.0 7.7 >>>> >>>>Based on the benchmark simulations, we can conclude that the scaling on >>>>LCRC can be linearly up to at least 256 CPU cores for our simulations. >>>> >>>> >>>> Requested: 400000 >>>> >>>>A specific reason has been given: >>>>We are currently using the AMBER molecular dynamics simulation package >>>>for polarizable simulations. We have observed some better agreements >>>>with >>>>experimental data using polarazable force field. Under AMBER, the >>>>program >>>>sander.MPI is used for the polarizable simulations. >>>>Based on our tests, the optimal performance is obtained when using 6 >>>>node >>>>with 16 cores per node. See the following for the results. With these >>>>test results, a total amount of allocation of 400,000 core hours is >>>>requests. >>>> >>>>#node (ppn=16): 2 3 4 5 6 7 >>>> 8 >>>>speed (ns/day) : 0.56 0.83 0.78 1.14 1.33 1.39 0.99 >>>> >>>> >>>>This needs to be approved and the final allocation amount decided upon. >>>> >>>>Thank You, >>>>The LCRC Accounts System >>> >>>_______________________________________________ >>>allocations-admins mailing list >>>allocations-admins(a)lcrc.anl.gov >>>https://lists.lcrc.anl.gov/mailman/listinfo/allocations-admins >> >>_______________________________________________ >>allocations-admins mailing list >>allocations-admins(a)lcrc.anl.gov >>https://lists.lcrc.anl.gov/mailman/listinfo/allocations-admins > >_______________________________________________ >allocations-admins mailing list >allocations-admins(a)lcrc.anl.gov >https://lists.lcrc.anl.gov/mailman/listinfo/allocations-admins >_______________________________________________ >allocations-admins mailing list >allocations-admins(a)lcrc.anl.gov >https://lists.lcrc.anl.gov/mailman/listinfo/allocations-admins

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Re: [allocations-admins] [LCRC Accounts] Project Allocation Request
by Low, John J. 27 May '15

27 May '15

Ray, Amber requires a $2000 license fee for computing centers in nonprofits. John J. Low Principal Computational Science Specialist Computing, Environment and Life Sciences Building 240, 2143 9700 South Cass Avenue Argonne National Laboratory Argonne, IL 60439. 630-252-0045 www.linkedin.com/pub/john-low/15/8b0/5aa/ ________________________________________ From: allocations-admins-bounces(a)lcrc.anl.gov [allocations-admins-bounces(a)lcrc.anl.gov] on behalf of Bair, Raymond A. [rbair(a)anl.gov] Sent: Wednesday, May 27, 2015 8:44 AM To: LCRC Allocations Admins Subject: Re: [allocations-admins] [LCRC Accounts] Project Allocation Request John, Did you see their comments about how the polarization model in Amber worked better for them? ----------------------------------------- Ray Bair Computing, Environment, and Life Sciences Argonne National Laboratory and the University of Chicago TCS Building 240, Room 4122 9700 South Cass Avenue Argonne, IL 60439 email: rbair(at)anl.gov Phone: (630)252-5751 On 5/26/15, 4:31 PM, "Low, John J." <jlow(a)mcs.anl.gov> wrote: >Ray, > >The authors of GROMACS are claiming a 3-5 speedup on gpus over a 6-core >haswell desktop (like my home system). Ellis, et al. could use the gpu >nodes on Blues or Fusion nodes. These nodes don’t seem to be heavily >used. > >See http://www.gromacs.org/GPU_acceleration. > >The GROMACS GPU benchmarks show good performance for models containing >100,000 or more atoms. If he is planning to use a model of that size, >then he could benefit by using the GPUs. > >John J. Low >Principal Computational Science Specialist >Computing, Environment and Life Sciences >Building 240, 2143 >9700 South Cass Avenue >Argonne National Laboratory >Argonne, IL 60439. >630-252-0045 >www.linkedin.com/pub/john-low/15/8b0/5aa/ > > > > > > >-----Original Message----- >From: <Bair>, "Bair, Raymond A." <rbair(a)anl.gov> >Reply-To: LCRC Allocations Admins <allocations-admins(a)lcrc.anl.gov> >Date: Tuesday, May 26, 2015 at 10:58 AM >To: "Ellis, Ross J." <rellis(a)anl.gov> >Cc: LCRC Allocations Admins <allocations-admins(a)lcrc.anl.gov> >Subject: Re: [allocations-admins] [LCRC Accounts] Project Allocation >Request > >>Dear Ross, >> >>At this time Blues is very full, so we have been asking projects to move >>to Fusion when they request large amounts of additional time in FY2015. >>Can your team use Fusion (8 cores per node) to do the proposed >>calculations? >> >>Also, for this size of a request we will need to poll the LCRC >>Allocations >>Committee. FYI, Al Wagner is your point of contact on this committee. >> >>Regards, >> >>Ray >> >>----------------------------------------- >>Ray Bair >>Computing, Environment, and Life Sciences >>Argonne National Laboratory >> and the University of Chicago >>TCS Building 240, Room 4122 >>9700 South Cass Avenue >>Argonne, IL 60439 >>email: rbair(at)anl.gov >>Phone: (630)252-5751 >> >> >> >> >> >>On 5/26/15, 10:46 AM, "accounts(a)lcrc.anl.gov" <accounts(a)lcrc.anl.gov> >>wrote: >> >>>Hello, >>> >>>A change in allocation has been requested: >>> >>> Requester: ellisrj (Ross Ellis) >>> Project: DMDOHEMA_1 >>> Title: Metal Ion Transport through Nano-Structured Lipophilic >>>Systems: Atomistic MD Simulations >>> Description: In the last few months, we have performed some >>>preliminary >>>simulation runs in understanding the supra-molecular aggregate structure >>>in organic phases under the project DMDOHEMA_1 on LCRC. Some findings >>>have been unveiled, e.g., the presences of water, acid, Eu(NO3)3 all >>>affect the supra-molecular aggregate structure of extractant (i.e., >>>DMDOHEMA) in organic phased. These findings agree with the existing >>>experimental data. However, due to the small size of those simulation >>>systems, the aggregation behaviors are not converged well. Therefore, in >>>the renewal period of project DMDOHEMA_1, we are aiming to enlarge our >>>simulation boxes so that such findings can be solidified. Moreover, one >>>already finished large simulation supports that larger simulation box >>>decreases the calculated error bar of the aggregation number of >>>DMDOHEMA. >>>With the simulations on large enough simulation boxes, the effects of >>>water, acid, Eu(NO3)3 will be distinguished, which will surely provi >>> de significant insight for the rational design of higher efficient >>>extractants. Our project is expected to highly spark the development of >>>rare earth element related technologies. >>>In this project, classical molecular dynamics (MD) simulations will be >>>performed at the all-atom resolution, in addition to the concurrent >>>solvent extraction experiments at ANL. All-atom MD simulations have been >>>well proven in predicting supra-molecular aggregate structures. The open >>>source package GROMACS will be employed for the simulations. GROMACS is >>>one of the highly recommended packages for MD simulations. GROMACS has >>>been reported to be able to scale well up to around 1,000 CPU >>>processors. >>>Based on our experience on LCRC, the simulations can be LINEARLY scaled >>>up to 256 CPU cores, under which condition the simulation speed is >>>around >>>3 hours/ns for a system of the size of around 17 Ã‹ 17 Ã‹ 17 = 5000 nm3. >>>Two users will use this allocation time, Dr. Ross J. Ellis and Dr. Baofu >>>Qiao, both at the CSE division at ANL. >>>In the first phase of this project, we are studying the influence of a >>>variety of components, i.e., water, acid, Eu(NO3)3, on the aggregate >>>structures of DMDOHEMA extractants dissolved in n-heptane organic >>>phases. >>>As aforementioned, this project is currently ongoing. With the >>>allocation >>>from LCRC, we are able to collects some conclusions in the near fure. >>>In the second phase, we plan to study the effect of extractant on the >>>supra-molecula aggregate structure. The extraction of DMDBTDMA, which is >>>the preceding extractant of DMDOHEMA, will be simulated and compared >>>with >>>the simulation results of DMDOHEMA systems. According to the available >>>experimental data, the effects of some factors will be explore, such as >>>the concentration of water, the concentration of Eu(NO3)3 complexes, the >>>concentration of acidic molecule of HNO3. >>> >>> >>> >>> Current: undetermined amount >>>Justification: Table. Benchmark of the simulation speed on LCRC >>>#CPU cores 16 32 64 256 >>>Speed >>>(ns/day) 0.51 1.0 2.0 7.7 >>> >>>Based on the benchmark simulations, we can conclude that the scaling on >>>LCRC can be linearly up to at least 256 CPU cores for our simulations. >>> >>> >>> Requested: 400000 >>> >>>A specific reason has been given: >>>We are currently using the AMBER molecular dynamics simulation package >>>for polarizable simulations. We have observed some better agreements >>>with >>>experimental data using polarazable force field. Under AMBER, the >>>program >>>sander.MPI is used for the polarizable simulations. >>>Based on our tests, the optimal performance is obtained when using 6 >>>node >>>with 16 cores per node. See the following for the results. With these >>>test results, a total amount of allocation of 400,000 core hours is >>>requests. >>> >>>#node (ppn=16): 2 3 4 5 6 7 >>> 8 >>>speed (ns/day) : 0.56 0.83 0.78 1.14 1.33 1.39 0.99 >>> >>> >>>This needs to be approved and the final allocation amount decided upon. >>> >>>Thank You, >>>The LCRC Accounts System >> >>_______________________________________________ >>allocations-admins mailing list >>allocations-admins(a)lcrc.anl.gov >>https://lists.lcrc.anl.gov/mailman/listinfo/allocations-admins > >_______________________________________________ >allocations-admins mailing list >allocations-admins(a)lcrc.anl.gov >https://lists.lcrc.anl.gov/mailman/listinfo/allocations-admins _______________________________________________ allocations-admins mailing list allocations-admins(a)lcrc.anl.gov https://lists.lcrc.anl.gov/mailman/listinfo/allocations-admins

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Re: [allocations-admins] [LCRC Accounts] Project Allocation Request
by Bair, Raymond A. 27 May '15

27 May '15

John, Did you see their comments about how the polarization model in Amber worked better for them? ----------------------------------------- Ray Bair Computing, Environment, and Life Sciences Argonne National Laboratory and the University of Chicago TCS Building 240, Room 4122 9700 South Cass Avenue Argonne, IL 60439 email: rbair(at)anl.gov Phone: (630)252-5751 On 5/26/15, 4:31 PM, "Low, John J." <jlow(a)mcs.anl.gov> wrote: >Ray, > >The authors of GROMACS are claiming a 3-5 speedup on gpus over a 6-core >haswell desktop (like my home system). Ellis, et al. could use the gpu >nodes on Blues or Fusion nodes. These nodes don’t seem to be heavily >used. > >See http://www.gromacs.org/GPU_acceleration. > >The GROMACS GPU benchmarks show good performance for models containing >100,000 or more atoms. If he is planning to use a model of that size, >then he could benefit by using the GPUs. > >John J. Low >Principal Computational Science Specialist >Computing, Environment and Life Sciences >Building 240, 2143 >9700 South Cass Avenue >Argonne National Laboratory >Argonne, IL 60439. >630-252-0045 >www.linkedin.com/pub/john-low/15/8b0/5aa/ > > > > > > >-----Original Message----- >From: <Bair>, "Bair, Raymond A." <rbair(a)anl.gov> >Reply-To: LCRC Allocations Admins <allocations-admins(a)lcrc.anl.gov> >Date: Tuesday, May 26, 2015 at 10:58 AM >To: "Ellis, Ross J." <rellis(a)anl.gov> >Cc: LCRC Allocations Admins <allocations-admins(a)lcrc.anl.gov> >Subject: Re: [allocations-admins] [LCRC Accounts] Project Allocation >Request > >>Dear Ross, >> >>At this time Blues is very full, so we have been asking projects to move >>to Fusion when they request large amounts of additional time in FY2015. >>Can your team use Fusion (8 cores per node) to do the proposed >>calculations? >> >>Also, for this size of a request we will need to poll the LCRC >>Allocations >>Committee. FYI, Al Wagner is your point of contact on this committee. >> >>Regards, >> >>Ray >> >>----------------------------------------- >>Ray Bair >>Computing, Environment, and Life Sciences >>Argonne National Laboratory >> and the University of Chicago >>TCS Building 240, Room 4122 >>9700 South Cass Avenue >>Argonne, IL 60439 >>email: rbair(at)anl.gov >>Phone: (630)252-5751 >> >> >> >> >> >>On 5/26/15, 10:46 AM, "accounts(a)lcrc.anl.gov" <accounts(a)lcrc.anl.gov> >>wrote: >> >>>Hello, >>> >>>A change in allocation has been requested: >>> >>> Requester: ellisrj (Ross Ellis) >>> Project: DMDOHEMA_1 >>> Title: Metal Ion Transport through Nano-Structured Lipophilic >>>Systems: Atomistic MD Simulations >>> Description: In the last few months, we have performed some >>>preliminary >>>simulation runs in understanding the supra-molecular aggregate structure >>>in organic phases under the project DMDOHEMA_1 on LCRC. Some findings >>>have been unveiled, e.g., the presences of water, acid, Eu(NO3)3 all >>>affect the supra-molecular aggregate structure of extractant (i.e., >>>DMDOHEMA) in organic phased. These findings agree with the existing >>>experimental data. However, due to the small size of those simulation >>>systems, the aggregation behaviors are not converged well. Therefore, in >>>the renewal period of project DMDOHEMA_1, we are aiming to enlarge our >>>simulation boxes so that such findings can be solidified. Moreover, one >>>already finished large simulation supports that larger simulation box >>>decreases the calculated error bar of the aggregation number of >>>DMDOHEMA. >>>With the simulations on large enough simulation boxes, the effects of >>>water, acid, Eu(NO3)3 will be distinguished, which will surely provi >>> de significant insight for the rational design of higher efficient >>>extractants. Our project is expected to highly spark the development of >>>rare earth element related technologies. >>>In this project, classical molecular dynamics (MD) simulations will be >>>performed at the all-atom resolution, in addition to the concurrent >>>solvent extraction experiments at ANL. All-atom MD simulations have been >>>well proven in predicting supra-molecular aggregate structures. The open >>>source package GROMACS will be employed for the simulations. GROMACS is >>>one of the highly recommended packages for MD simulations. GROMACS has >>>been reported to be able to scale well up to around 1,000 CPU >>>processors. >>>Based on our experience on LCRC, the simulations can be LINEARLY scaled >>>up to 256 CPU cores, under which condition the simulation speed is >>>around >>>3 hours/ns for a system of the size of around 17 Ã‹ 17 Ã‹ 17 = 5000 nm3. >>>Two users will use this allocation time, Dr. Ross J. Ellis and Dr. Baofu >>>Qiao, both at the CSE division at ANL. >>>In the first phase of this project, we are studying the influence of a >>>variety of components, i.e., water, acid, Eu(NO3)3, on the aggregate >>>structures of DMDOHEMA extractants dissolved in n-heptane organic >>>phases. >>>As aforementioned, this project is currently ongoing. With the >>>allocation >>>from LCRC, we are able to collects some conclusions in the near fure. >>>In the second phase, we plan to study the effect of extractant on the >>>supra-molecula aggregate structure. The extraction of DMDBTDMA, which is >>>the preceding extractant of DMDOHEMA, will be simulated and compared >>>with >>>the simulation results of DMDOHEMA systems. According to the available >>>experimental data, the effects of some factors will be explore, such as >>>the concentration of water, the concentration of Eu(NO3)3 complexes, the >>>concentration of acidic molecule of HNO3. >>> >>> >>> >>> Current: undetermined amount >>>Justification: Table. Benchmark of the simulation speed on LCRC >>>#CPU cores 16 32 64 256 >>>Speed >>>(ns/day) 0.51 1.0 2.0 7.7 >>> >>>Based on the benchmark simulations, we can conclude that the scaling on >>>LCRC can be linearly up to at least 256 CPU cores for our simulations. >>> >>> >>> Requested: 400000 >>> >>>A specific reason has been given: >>>We are currently using the AMBER molecular dynamics simulation package >>>for polarizable simulations. We have observed some better agreements >>>with >>>experimental data using polarazable force field. Under AMBER, the >>>program >>>sander.MPI is used for the polarizable simulations. >>>Based on our tests, the optimal performance is obtained when using 6 >>>node >>>with 16 cores per node. See the following for the results. With these >>>test results, a total amount of allocation of 400,000 core hours is >>>requests. >>> >>>#node (ppn=16): 2 3 4 5 6 7 >>> 8 >>>speed (ns/day) : 0.56 0.83 0.78 1.14 1.33 1.39 0.99 >>> >>> >>>This needs to be approved and the final allocation amount decided upon. >>> >>>Thank You, >>>The LCRC Accounts System >> >>_______________________________________________ >>allocations-admins mailing list >>allocations-admins(a)lcrc.anl.gov >>https://lists.lcrc.anl.gov/mailman/listinfo/allocations-admins > >_______________________________________________ >allocations-admins mailing list >allocations-admins(a)lcrc.anl.gov >https://lists.lcrc.anl.gov/mailman/listinfo/allocations-admins

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Re: [allocations-admins] [LCRC Accounts] Project Allocation Request
by Low, John J. 26 May '15

26 May '15

Ray, The authors of GROMACS are claiming a 3-5 speedup on gpus over a 6-core haswell desktop (like my home system). Ellis, et al. could use the gpu nodes on Blues or Fusion nodes. These nodes don’t seem to be heavily used. See http://www.gromacs.org/GPU_acceleration. The GROMACS GPU benchmarks show good performance for models containing 100,000 or more atoms. If he is planning to use a model of that size, then he could benefit by using the GPUs. John J. Low Principal Computational Science Specialist Computing, Environment and Life Sciences Building 240, 2143 9700 South Cass Avenue Argonne National Laboratory Argonne, IL 60439. 630-252-0045 www.linkedin.com/pub/john-low/15/8b0/5aa/ -----Original Message----- From: <Bair>, "Bair, Raymond A." <rbair(a)anl.gov> Reply-To: LCRC Allocations Admins <allocations-admins(a)lcrc.anl.gov> Date: Tuesday, May 26, 2015 at 10:58 AM To: "Ellis, Ross J." <rellis(a)anl.gov> Cc: LCRC Allocations Admins <allocations-admins(a)lcrc.anl.gov> Subject: Re: [allocations-admins] [LCRC Accounts] Project Allocation Request >Dear Ross, > >At this time Blues is very full, so we have been asking projects to move >to Fusion when they request large amounts of additional time in FY2015. >Can your team use Fusion (8 cores per node) to do the proposed >calculations? > >Also, for this size of a request we will need to poll the LCRC Allocations >Committee. FYI, Al Wagner is your point of contact on this committee. > >Regards, > >Ray > >----------------------------------------- >Ray Bair >Computing, Environment, and Life Sciences >Argonne National Laboratory > and the University of Chicago >TCS Building 240, Room 4122 >9700 South Cass Avenue >Argonne, IL 60439 >email: rbair(at)anl.gov >Phone: (630)252-5751 > > > > > >On 5/26/15, 10:46 AM, "accounts(a)lcrc.anl.gov" <accounts(a)lcrc.anl.gov> >wrote: > >>Hello, >> >>A change in allocation has been requested: >> >> Requester: ellisrj (Ross Ellis) >> Project: DMDOHEMA_1 >> Title: Metal Ion Transport through Nano-Structured Lipophilic >>Systems: Atomistic MD Simulations >> Description: In the last few months, we have performed some preliminary >>simulation runs in understanding the supra-molecular aggregate structure >>in organic phases under the project DMDOHEMA_1 on LCRC. Some findings >>have been unveiled, e.g., the presences of water, acid, Eu(NO3)3 all >>affect the supra-molecular aggregate structure of extractant (i.e., >>DMDOHEMA) in organic phased. These findings agree with the existing >>experimental data. However, due to the small size of those simulation >>systems, the aggregation behaviors are not converged well. Therefore, in >>the renewal period of project DMDOHEMA_1, we are aiming to enlarge our >>simulation boxes so that such findings can be solidified. Moreover, one >>already finished large simulation supports that larger simulation box >>decreases the calculated error bar of the aggregation number of DMDOHEMA. >>With the simulations on large enough simulation boxes, the effects of >>water, acid, Eu(NO3)3 will be distinguished, which will surely provi >> de significant insight for the rational design of higher efficient >>extractants. Our project is expected to highly spark the development of >>rare earth element related technologies. >>In this project, classical molecular dynamics (MD) simulations will be >>performed at the all-atom resolution, in addition to the concurrent >>solvent extraction experiments at ANL. All-atom MD simulations have been >>well proven in predicting supra-molecular aggregate structures. The open >>source package GROMACS will be employed for the simulations. GROMACS is >>one of the highly recommended packages for MD simulations. GROMACS has >>been reported to be able to scale well up to around 1,000 CPU processors. >>Based on our experience on LCRC, the simulations can be LINEARLY scaled >>up to 256 CPU cores, under which condition the simulation speed is around >>3 hours/ns for a system of the size of around 17 Ã‹ 17 Ã‹ 17 = 5000 nm3. >>Two users will use this allocation time, Dr. Ross J. Ellis and Dr. Baofu >>Qiao, both at the CSE division at ANL. >>In the first phase of this project, we are studying the influence of a >>variety of components, i.e., water, acid, Eu(NO3)3, on the aggregate >>structures of DMDOHEMA extractants dissolved in n-heptane organic phases. >>As aforementioned, this project is currently ongoing. With the allocation >>from LCRC, we are able to collects some conclusions in the near fure. >>In the second phase, we plan to study the effect of extractant on the >>supra-molecula aggregate structure. The extraction of DMDBTDMA, which is >>the preceding extractant of DMDOHEMA, will be simulated and compared with >>the simulation results of DMDOHEMA systems. According to the available >>experimental data, the effects of some factors will be explore, such as >>the concentration of water, the concentration of Eu(NO3)3 complexes, the >>concentration of acidic molecule of HNO3. >> >> >> >> Current: undetermined amount >>Justification: Table. Benchmark of the simulation speed on LCRC >>#CPU cores 16 32 64 256 >>Speed >>(ns/day) 0.51 1.0 2.0 7.7 >> >>Based on the benchmark simulations, we can conclude that the scaling on >>LCRC can be linearly up to at least 256 CPU cores for our simulations. >> >> >> Requested: 400000 >> >>A specific reason has been given: >>We are currently using the AMBER molecular dynamics simulation package >>for polarizable simulations. We have observed some better agreements with >>experimental data using polarazable force field. Under AMBER, the program >>sander.MPI is used for the polarizable simulations. >>Based on our tests, the optimal performance is obtained when using 6 node >>with 16 cores per node. See the following for the results. With these >>test results, a total amount of allocation of 400,000 core hours is >>requests. >> >>#node (ppn=16): 2 3 4 5 6 7 >> 8 >>speed (ns/day) : 0.56 0.83 0.78 1.14 1.33 1.39 0.99 >> >> >>This needs to be approved and the final allocation amount decided upon. >> >>Thank You, >>The LCRC Accounts System > >_______________________________________________ >allocations-admins mailing list >allocations-admins(a)lcrc.anl.gov >https://lists.lcrc.anl.gov/mailman/listinfo/allocations-admins

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[LCRC Accounts] Project Request: Irridates
by accounts＠lcrc.anl.gov 26 May '15

26 May '15

Hello, A new project on the LCRC cluster has been requested. Please forward the information on to the LCRC Allocation sub-committee. Applicant's name: Peter Littlewood Applicant's institution: ANL Applicant's division: PSE Project Name: Irridates Project title: Metal-insulator phase transitions in irridates Associated funding: DoE Other Systems: Science: Our goal is to investigate the role of the rare earth elements (R) in metal-insulator transitions of pyrochlore irridate compounds. Contrary to what expected, the R-dependence in a single-site DMFT calculation with local Coulomb interaction is very weak. We want to perform cluster DMFT calculations for three irridate compounds (Lu, Y, and Eu) with configuration-interaction-based exact diagonalization solvers. Project description: We will use MPI Fortran codes developed at Coulumbia University at NYC. Based on previous cluster DMFT calculations for a model tight binding Hamiltonian we estimate the CPU hours for a submitted job as 10k: 12 nodes * 16 cores per node (Blues) running for 48 hours. The work will be divided in multiple sets containing external parameters. Considering the limited resources, we will target parameters to solve instead of surveying entire phase diagram. Previous tests using thousands of cores simultaneously indicate that a better performance is achieved running jobs on hundreds of cores. The project is expected to have three members at most. Industry partnership: Project URL: Requested allocation: 350000 Q1: 0 Q2: 0 Q3: 0 Q4: 350000 Justification: Storage requirements: less that 1 TB The requester has used undetermined amount hours of their initial startup project. In addition to approving an initial amount, please specify a Category and Subcategory for this project. For a list of the current selection of approved categories, please see: https://wiki.lcrc.anl.gov/wiki/Processes/Categories Once the Allocation committee has approved the project, please go to the Project Management page to create it: https://accounts.lcrc.anl.gov/projects.php Thank You, The LCRC Accounts System

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Re: [allocations-admins] [LCRC Accounts] Project Allocation Request
by Bair, Raymond A. 26 May '15

26 May '15

Dear Ross, At this time Blues is very full, so we have been asking projects to move to Fusion when they request large amounts of additional time in FY2015. Can your team use Fusion (8 cores per node) to do the proposed calculations? Also, for this size of a request we will need to poll the LCRC Allocations Committee. FYI, Al Wagner is your point of contact on this committee. Regards, Ray ----------------------------------------- Ray Bair Computing, Environment, and Life Sciences Argonne National Laboratory and the University of Chicago TCS Building 240, Room 4122 9700 South Cass Avenue Argonne, IL 60439 email: rbair(at)anl.gov Phone: (630)252-5751 On 5/26/15, 10:46 AM, "accounts(a)lcrc.anl.gov" <accounts(a)lcrc.anl.gov> wrote: >Hello, > >A change in allocation has been requested: > > Requester: ellisrj (Ross Ellis) > Project: DMDOHEMA_1 > Title: Metal Ion Transport through Nano-Structured Lipophilic >Systems: Atomistic MD Simulations > Description: In the last few months, we have performed some preliminary >simulation runs in understanding the supra-molecular aggregate structure >in organic phases under the project DMDOHEMA_1 on LCRC. Some findings >have been unveiled, e.g., the presences of water, acid, Eu(NO3)3 all >affect the supra-molecular aggregate structure of extractant (i.e., >DMDOHEMA) in organic phased. These findings agree with the existing >experimental data. However, due to the small size of those simulation >systems, the aggregation behaviors are not converged well. Therefore, in >the renewal period of project DMDOHEMA_1, we are aiming to enlarge our >simulation boxes so that such findings can be solidified. Moreover, one >already finished large simulation supports that larger simulation box >decreases the calculated error bar of the aggregation number of DMDOHEMA. >With the simulations on large enough simulation boxes, the effects of >water, acid, Eu(NO3)3 will be distinguished, which will surely provi > de significant insight for the rational design of higher efficient >extractants. Our project is expected to highly spark the development of >rare earth element related technologies. >In this project, classical molecular dynamics (MD) simulations will be >performed at the all-atom resolution, in addition to the concurrent >solvent extraction experiments at ANL. All-atom MD simulations have been >well proven in predicting supra-molecular aggregate structures. The open >source package GROMACS will be employed for the simulations. GROMACS is >one of the highly recommended packages for MD simulations. GROMACS has >been reported to be able to scale well up to around 1,000 CPU processors. >Based on our experience on LCRC, the simulations can be LINEARLY scaled >up to 256 CPU cores, under which condition the simulation speed is around >3 hours/ns for a system of the size of around 17 Ã‹ 17 Ã‹ 17 = 5000 nm3. >Two users will use this allocation time, Dr. Ross J. Ellis and Dr. Baofu >Qiao, both at the CSE division at ANL. >In the first phase of this project, we are studying the influence of a >variety of components, i.e., water, acid, Eu(NO3)3, on the aggregate >structures of DMDOHEMA extractants dissolved in n-heptane organic phases. >As aforementioned, this project is currently ongoing. With the allocation >from LCRC, we are able to collects some conclusions in the near fure. >In the second phase, we plan to study the effect of extractant on the >supra-molecula aggregate structure. The extraction of DMDBTDMA, which is >the preceding extractant of DMDOHEMA, will be simulated and compared with >the simulation results of DMDOHEMA systems. According to the available >experimental data, the effects of some factors will be explore, such as >the concentration of water, the concentration of Eu(NO3)3 complexes, the >concentration of acidic molecule of HNO3. > > > > Current: undetermined amount >Justification: Table. Benchmark of the simulation speed on LCRC >#CPU cores 16 32 64 256 >Speed >(ns/day) 0.51 1.0 2.0 7.7 > >Based on the benchmark simulations, we can conclude that the scaling on >LCRC can be linearly up to at least 256 CPU cores for our simulations. > > > Requested: 400000 > >A specific reason has been given: >We are currently using the AMBER molecular dynamics simulation package >for polarizable simulations. We have observed some better agreements with >experimental data using polarazable force field. Under AMBER, the program >sander.MPI is used for the polarizable simulations. >Based on our tests, the optimal performance is obtained when using 6 node >with 16 cores per node. See the following for the results. With these >test results, a total amount of allocation of 400,000 core hours is >requests. > >#node (ppn=16): 2 3 4 5 6 7 > 8 >speed (ns/day) : 0.56 0.83 0.78 1.14 1.33 1.39 0.99 > > >This needs to be approved and the final allocation amount decided upon. > >Thank You, >The LCRC Accounts System

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[LCRC Accounts] Project Allocation Request
by accounts＠lcrc.anl.gov 26 May '15

26 May '15

Hello, A change in allocation has been requested: Requester: ellisrj (Ross Ellis) Project: DMDOHEMA_1 Title: Metal Ion Transport through Nano-Structured Lipophilic Systems: Atomistic MD Simulations Description: In the last few months, we have performed some preliminary simulation runs in understanding the supra-molecular aggregate structure in organic phases under the project DMDOHEMA_1 on LCRC. Some findings have been unveiled, e.g., the presences of water, acid, Eu(NO3)3 all affect the supra-molecular aggregate structure of extractant (i.e., DMDOHEMA) in organic phased. These findings agree with the existing experimental data. However, due to the small size of those simulation systems, the aggregation behaviors are not converged well. Therefore, in the renewal period of project DMDOHEMA_1, we are aiming to enlarge our simulation boxes so that such findings can be solidified. Moreover, one already finished large simulation supports that larger simulation box decreases the calculated error bar of the aggregation number of DMDOHEMA. With the simulations on large enough simulation boxes, the effects of water, acid, Eu(NO3)3 will be distinguished, which will surely provi de significant insight for the rational design of higher efficient extractants. Our project is expected to highly spark the development of rare earth element related technologies. In this project, classical molecular dynamics (MD) simulations will be performed at the all-atom resolution, in addition to the concurrent solvent extraction experiments at ANL. All-atom MD simulations have been well proven in predicting supra-molecular aggregate structures. The open source package GROMACS will be employed for the simulations. GROMACS is one of the highly recommended packages for MD simulations. GROMACS has been reported to be able to scale well up to around 1,000 CPU processors. Based on our experience on LCRC, the simulations can be LINEARLY scaled up to 256 CPU cores, under which condition the simulation speed is around 3 hours/ns for a system of the size of around 17 × 17 × 17 = 5000 nm3. Two users will use this allocation time, Dr. Ross J. Ellis and Dr. Baofu Qiao, both at the CSE division at ANL. In the first phase of this project, we are studying the influence of a variety of components, i.e., water, acid, Eu(NO3)3, on the aggregate structures of DMDOHEMA extractants dissolved in n-heptane organic phases. As aforementioned, this project is currently ongoing. With the allocation from LCRC, we are able to collects some conclusions in the near fure. In the second phase, we plan to study the effect of extractant on the supra-molecula aggregate structure. The extraction of DMDBTDMA, which is the preceding extractant of DMDOHEMA, will be simulated and compared with the simulation results of DMDOHEMA systems. According to the available experimental data, the effects of some factors will be explore, such as the concentration of water, the concentration of Eu(NO3)3 complexes, the concentration of acidic molecule of HNO3. Current: undetermined amount Justification: Table. Benchmark of the simulation speed on LCRC #CPU cores 16 32 64 256 Speed (ns/day) 0.51 1.0 2.0 7.7 Based on the benchmark simulations, we can conclude that the scaling on LCRC can be linearly up to at least 256 CPU cores for our simulations. Requested: 400000 A specific reason has been given: We are currently using the AMBER molecular dynamics simulation package for polarizable simulations. We have observed some better agreements with experimental data using polarazable force field. Under AMBER, the program sander.MPI is used for the polarizable simulations. Based on our tests, the optimal performance is obtained when using 6 node with 16 cores per node. See the following for the results. With these test results, a total amount of allocation of 400,000 core hours is requests. #node (ppn=16): 2 3 4 5 6 7 8 speed (ns/day) : 0.56 0.83 0.78 1.14 1.33 1.39 0.99 This needs to be approved and the final allocation amount decided upon. Thank You, The LCRC Accounts System

1 0