XUP

RE: Startup allocation request submission error

2022-08-17T18:40:35Z

I tried to find where I was wrong to fix it, but I can't find. My role is" Allocation manager", and I set up my supervisor's role as PI.Isn't it possible that allocation manager can submit the startup allocation request?

Bugarsky & Navarro, LLC

VIVA99 Slot Online Gacor

2022-07-07T15:28:47Z

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Imaging Informatics Engineer Job at UF

2022-06-21T13:40:19Z

The University of Florida invites applications for an
Imaging Informatics Engineer
to support imaging data for research and innovation.
Apply Here
Brief Description
This position will be responsible for:
● Manage clinical imaging data and pipelines that support cutting-edge data science and artificial intelligence (AI) research and innovation
● Collaborating closely with clinical and informatics teams across the University of Florida

Full Description
This position will architect and continually improve processes to extract, curate, and analyze clinical imaging data in a dynamic research environment at a top 5 public research institution. The position will be key to developing imaging informatics data systems that contribute to the university and health system’s aim to be world leaders in artificial intelligence (AI) methods and applications. This position will work closely with UF data scientists and clinical researchers, and with partner organizations, like NVIDIA. The position will collaborate with research imaging teams across campus such as the Norman Fixel Institute for Neurological Diseases and the McKnight Brain Institute.
The position will develop one or more imaging informatics platforms, using XNAT and other imaging informatics tools, to ensure secure and high-quality imaging data extraction from health system imaging archives and delivery to research computing environments. This position is expected to learn from and engage with local, national, and global informatics communities with an emphasis on AI activities.

Globus XSEDE

2022-06-13T16:28:40Z

Hello,

I want to connect into Globus through XSEDE in Python. It generally requires "Multi-Factor Authentication" and we have to enter an authorized phone number.
My questions:
1) Is there anyway to connect to connect without Multi-Factor Authentication?
2) Is there any sample Python code that I could connect into Globus via XSEDE authentication?

Thanks a lot.

RE: ABAQUS license information

2022-01-23T18:06:52Z

Hi Xiaofan, did you ever figure this out? I'm trying to get approved on Stampede2 for use of a software package as well.

Running MapReduce on multicore in hadoop 2.6

2021-09-07T21:27:08Z

I am trying to run a MapReduce application in a single node machine and utilize its multicore to act as mapper and reducer. I am setting it in the following way:

Configuration conf = new Configuration();
conf.set("mapreduce.tasktracker.map.tasks.maximum", String.valueOf(NO_OF_MAPPERS));
conf.set("mapreduce.tasktracker.reduce.tasks.maximum", String.valueOf(NO_OF_REDUCERS));

I am not sure whether I am doing it right because I don't see any performance increase by using a higher number of mappers and reducers. Can anyone help me? Any help is highly appreciated.

problem with mpi on stampede2 - ifort fflags?

2021-09-07T17:40:06Z

Dear all,

I am trying to run the ROMS ocean model on stampede2
I am able to get it run using openmp, but I am having trouble making it run using mpi.

Compiling does not complain (using ifort / mpfi90 / mvapich2. see below for flags)

When I run however I get the following errors (depending on the mpfi90 flags):

forrtl: severe (194): Run-Time Check Failure. The variable 'distribute_mod_mp_mp_reduce_1d_$SERROR' is being used in 'distribute.f90(4812,19)' without being defined
when I use the following fflags:
mpif90 -c -fp-model precise -heap-arrays -ip -O3 -traceback -check uninit

or

Fatal error in PMPI_Bcast: Message truncated, error stack:
PMPI_Bcast(1645)............: MPI_Bcast(buf=0x2b6bf2e372e0, count=20, MPI_DOUBLE_PRECISION, root=0, MPI_COMM_WORLD) failed
when I use the following fflags:
mpif90 -c -fp-model precise -heap-arrays -ip -O3

I am guessing that I cannot run it because I don't have the right flags for mpi.

any help and tips are greatly appreciated !

Vincent

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2021-07-28T12:18:07Z

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Running replica exchange jobs on bridges2 GPU

2021-07-23T20:32:01Z

Hi,

I am attempting to run my replica exchange jobs using NAMD on GPU nodes. Usually this involves mpirun or charmrun, but I can't seem to use either of these programs when loading namd/2.13-gpu.

Can someone suggest how I might do this. My example job file is below.

Thanks,
Jackson

#!/bin/bash
#SBATCH -N 1
#SBATCH --ntasks-per-node=40
#SBATCH -p GPU
#SBATCH -t 0:30
#SBATCH --gres=gpu:v100:8
#
set echo
set -x
# Load the needed modules
module load namd/2.13-gpu
cd $PROJECT/charmm-ccl5-r2/namd
echo $SLURM_NTASKS
#
mkdir output
for n in $( seq 0 $((${SLURM_NTASKS}-1)) ); do
mkdir -p output/${n}
done
#

charmrun $BINDIR/namd2 +p ${SLURM_NTASKS} +replicas ${SLURM_NTASKS} job0.conf +stdout output/%d/job0.%d.log

How to access GROMACS in Expanse

2021-07-20T21:20:33Z

I found that GROMACS 2019 and 2020 are available in Expanse. I was trying to access it by loading all the necessary modules. However, after loading the required modules including gromacs/2019.6, I was able to get gmx_mpi executable but unable to run simple commands like gmx_mpi -version etc. It is showing the following error-

By default, for Open MPI 4.0 and later, infiniband ports on a device
are not used by default. The intent is to use UCX for these devices.
You can override this policy by setting the btl_openib_allow_ib MCA parameter
to true.

Local host: exp-7-60
Local adapter: mlx5_0
Local port: 1

--------------------------------------------------------------------------
--------------------------------------------------------------------------
WARNING: There was an error initializing an OpenFabrics device.

Local host: exp-7-60
Local device: mlx5_0
--------------------------------------------------------------------------
srun: error: PMK_KVS_Barrier duplicate request from task 0

Here are the currently loaded modules-
Currently Loaded Modules:
1) shared 2) DefaultModules 3) gpu/0.15.4 4) openmpi/4.0.4 5) slurm/expanse/20.02.3 6) sdsc/1.0 7) gromacs/2019.6

Inactive Modules:
1) gcc/10.2.0

I would appreciate if anyone can tell me how to run gromacs job in Expanse.
Thanks,
Sanjoy Paul
Boston University
email: sanjoypaul25@gmail.com

RE: How to handle dynamic IP

2021-05-25T18:17:03Z

Hi,

I think your question would be better answered by submitting a consulting ticket to the Jetstream team:

https://portal.xsede.org/group/xup/help-desk

Maytal

How to handle dynamic IP

2021-05-25T16:58:47Z

Hello I've got a few apps pointing to a Postgres database hosted on a Jetstream allocation. The IP# number has changed from 6 months ago and I'm having to fix a number of links.
Would a dynamic DNS service like dynu.com provide an alias I could use?
I'm hoping for a single place to update the IP# and all the links would be corrected.

Allocations (Transfer)

2021-05-16T15:28:42Z

Hello,

I have been reading the documentation on Managing Allocations, in particular "Transfer Between Resources"
I would like to transfer from Comet to Expanse, I have gone to the submit/review under XRAS and clicked the "Transfer". I know which resource to transfer to but I would like to transfer only X number of SU's --> can this be specified when I click "Start Transfer" or will it transfer all my compute SU's from Comet to Expanse.
More generally, is there a guide for accomplishing this? I received several messages about the transfer from Comet to Expanse (comet is being decommissioned); however, I cannot find a guide/web video about transfering the resources.

Thanks.

How to use blastx

2021-05-13T15:10:49Z

Hello,

I want to run blastx on xsede.

I have a multifasta file containing ~90,000 sequences.

I do not have any coding experience. I am wondering if there are ways to run the blastx on my multifasta file.

Your help is much appreciated.

Regards,
SD

RE: User missing directory in /expanse/lustre/projects

2020-12-16T18:04:49Z

Please submit a ticket to help@xsede.org and they can help look at your account users and contact Expanse.

Running Jobs

2020-12-01T07:28:58Z

Good Morning

My name is Amnah and I am new in XSEDE. I am trying to submit a job through Bridges. I need to use GROMACS

I have watched the training videos and the user guide but the instruction to submit the jobs was not clear enough for me If you could provide me a systematic instruction to guide me and possible templates of the batch file to use in order to submit a gob, I will appreciate that.

Thanks in advance

Startup allocation co-PI

2020-09-11T15:48:02Z

Good Morning,

I am planning on sending a startup allocation project and my collaborator is based at a non-US institution. I would like to know if it is possible to add him as a co-PI of the project.

Bridges: Processing large number of large files

2020-08-13T20:28:57Z

Hey guys,

Do you have suggestions on best way to submitting batch job on Bridges for a project with large number of large file?

I have a projects where I need to process around 100,000 csv.gz. An average gz file is 500 MB. I am currently processing with grep | sed | awk. So approximately for each file the processing time is 0.5 hour on a RM-shared core.

My thinking on this is that I submit 100,000 RM-shared batch where each batch process one file. But my concern is that my later jobs will have lower priority since I have already submitted/completed many jobs.

I cannot find such mechanism in PSC documentation but I think it's a common thing for supercomputers. Can anyone help me verify that? Also any suggestions are welcome.

ABAQUS license information

2020-08-04T19:44:43Z

Hello all,

I understand that we need to have our own licenses to run abaqus on XSEDE. Does anyone know where and how we can enter the abaqus license information when we submit abaqus jobs? Is there any configuration/input files we can reference our license information?

Thanks for your help,
Xiaofan

GC Overhead limit exceeded error in Hadoop

2020-07-30T09:13:38Z

I am working on a Hadoop Map/Reduce application. In one of the experiments with a large data set, I got an error saying that GC overhead limit exceeded. Can anyone tell me what could be the reason and how can I solve it in Hadoop?