How to handle dynamic IP

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

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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.

Flash scratch storage - what happens if job runs out of walltime?

2022-05-12T21:24:03Z

Hi all,

I currently have a trial allocation on expanse and I am trying to get my software (ORCA) configured as best as possible before I run some benchmarks.

Often I am running restartable jobs, and will run out of walltime and need to resubmit the job. I would like to use the SSD flash scratch storage to hold my running jobs, the storage that is accessed under "/scratch/$USER/job/$SLURM_JOB_ID". The guide specifies this is only accessible during a job run. Obviously, after the job is done, whether it finishes successfully or fails, it goes to my next command in the slurm script which is to move all of the data back to home directory. But if it runs out of walltime while ORCA is still running, that next command to move the data back to home will not run. I was wondering what I can do to ensure that I am not wasting my SUs of that job by losing all of the data.

Other clusters have a "orphan" folder where this lost data is sometimes held for a time. Do XSEDE clusters or expanse have an option like this?

Alternatively, I have used epilog scripts before in TORQUE, and I know SLURM also has the option of epilog scripts. Will an epilog script have access to that scratch folder, and if so can I use an epilog script to copy it back so that it will always copy whether the job runs out of walltime or not?

Help with `srun nvidia-smi` for power measurements

2022-04-27T14:25:43Z

I'm currently writing a script to get power measurements from the NVIDIA V100 GPU on Expanse-GPU (SDSC). Out of the three methods possible (`nvidia-smi`, NVML, and CUPTI), it seems that `nvidia-smi` has the lowest barrier to entry because it comes with the NVIDIA drivers.

Currently I have the following three concerns:

1. How to deal with Slurm.
For some reason, at Expanse-GPU, after getting an interactive node on the `gpu-shared` partition (or any other Expanse-GPU partition, for that matter) , you can only run `srun nvidia-smi` but not `nvidia-smi` directly. This suggests that either Expanse has a three-tiered node hierarchy (login, batch, compute) like Summit, or for some reason the environment isn't setup properly outside of `srun`. Which one of these two scenarios is true?

2. How to spawn and kill `nvidia-smi` properly.
This is a technical aspect, but I'm not sure how to reliably spawn and kill (or start and stop) `nvidia-smi` in the Slurm job script. I am only mildly familiar with `pidof` and `kill`.

3. How to set polling interval appropriately.
This is more of a conceptual thing. In quantum physics, a measurement changes the system. I think a similar concept applies here since we're polling the GPU by using `nvidia-smi`. If the frequency is too high, we might incur a performance cost. If the frequency is too low, the data will be inaccurate and the program to be analyzed might finish entirely within the polling interval. How can I determine the appropriate polling interval?

I have also submitted ticket #21526 to the Expanse help desk.

RE: Research Allocation Limits on Bridges-2 RM and Bridges-2 EM

2022-04-11T23:46:14Z

Hi Gowri,

There are no limits on what can be requested for any XSEDE allocated resource in a Research request. If you can justify the need, please request this amount of SUs. There may be some limits based on supply and demand but that will be decided at the review meeting and the amount of SUs the sites like PSC will make available. PSC normally makes 127M SUs available on Bridges-2 RM per quarter.

More information about Research allocations can be found:

https://portal.xsede.org/allocations/research

Please send any questions to help@xsede.org as you proceed with preparing your allocation request.

Ken Hackworth
XSEDE Allocations

Research Allocation Limits on Bridges-2 RM and Bridges-2 EM

2022-04-11T23:20:55Z

Hi,

What is the research allocation limit on Bridges-2 nodes?

I looked at the resource information page, https://portal.xsede.org/allocations/resource-info, but only the startup allocation limits are listed there. Are these limits the same for research allocations?

Thank you,
Gowri

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.

Image rendering for data visualization

2021-12-09T18:51:21Z

Is there a way I can remotely using CPU or GPU resources for rendering still 3D images (and video eventually) while still using my own computer and graphics program? I'm very new to this and not sure how it would work.

RE: XRAC Allocations Starting 04-01-2014

2021-11-02T08:14:22Z

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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

RE: Allocation end date extension

2021-07-31T20:18:19Z

Hello Iana,

It is possible to extend an allocation, you will want to go to the XSEDE Allocation submission site:

https://portal.xsede.org/submit-request#/

there you should see your current allocation along with a blue Action button, select this and you should see the option for Extension.

Hope this helps.

Ken Hackworth
XSEDE Allocations

Allocation end date extension

2021-07-31T19:50:34Z

Hello everyone!

I have a question related to the allocation's expiration period. My research group is using the computational recourses on both Bridges and Expanse clusters. However, we will be not able to use all the recourses by the allocation deadline which is September 30. Is there a way to extend the allocation deadline period so we can continue using our recourses instead of writing a new allocation proposal?

Thank you for your time and consideration.

Sincerely,

Iana

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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.