Questions tagged [hpc]

High Performance Computing encompasses using "supercomputers" with high numbers of CPUs, large parallel storage systems and advanced networks to perform time-consuming calculations. Parallel algorithms and parallelization of storage are essential to this field, as well as issues with complex, fast networking fabrics such as Infiniband.

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Latency of memory accesses via interconnectors

I'm trying to compare latencies of different node interconnects for a cluster. The goal is to minimize the memory access latency. I have obtained some benchmarks regarding one of the hardware ...
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Current single system image solutions

I'm designing a cluster for a small research institute. Since our computations require a large amount of memory, I'm looking for a solution that will allow our applications access to the whole memory ...
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125 views

ssh port forwarding (tunneling in HPC)

I have an application server that runs on a compute node. The server opens a port (9000) and I then run a command for tunneling between my local machine and the server: ssh -N -f -L 9000:compute-node:...
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27 views

HPC cluster master node as virtual machine

For a given small HPC cluster (~16 nodes) a master node is used as a front-end for users to login and interact with SLURM, and not as a computing node. The master node is currently a bare-metal server....
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87 views

OpenLDAP implementation allows only root user to set passwords of accounts

I'm working application that requires the use of AWS ParallelCluster assets for some high performance processing. After the initial setup, we need to be able to add/remove user accounts and I am ...
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347 views

Considerations using consumer class (high-end) GPU in server?

Motivation: First of all, even if I have some knowledge of computer science, software development and server Linux administration, I never looked into a server hardware and I am a total "newbie&...
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Infiniband drivers : OFED or distro included?

I'm setting up a Linux cluster with infiniband network, and I'm quite a newby in infiniband wolrd, any advice is more than welcome ! We are currently using Mellanox OFED drivers, but our infiniband ...
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SLURM with “partial” head node

I am trying to install SLURM with NFS on a small ubuntu 18.04 HPC cluster, in a typical fashion, e.g. configure controller (slurmctld) and clients (slurmd) and shared directory, etc. What I am curious ...
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Bad multicore performance on DL360 Gen 10 with 2xXeon 6154

I have some issue on the multi-core performance of some server. The server are HPE DL360 Gen10, mounting 2x Xeon Gold 6154 (18 cores). When i refer to the performances they are slower then some older ...
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2answers
171 views

What is the overhead of ZFS RAIDz1/2 in HPC SSD Environment?

Example hardware / host: Modern 64 Core CPU, 128GB Memory 8 x Micron Pro 15.36TB u.2 SSDs SSDs connected by dedicated Oculink per device (no backplane or PCIe sharing) Ubuntu 20.04 Use case: A ...
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306 views

Wrong LDAP user ID is mapped into Slurm account management service

I configured a Slurm head node as follows: sssd to contact openLDAP slurmctld/slurmdbd/slurmd/munged to act as the Slurm controller and compute node ...where ray.williams is an LDAP user. Its UID ...
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218 views

HTCondor high availability

I am currently trying to make the job queue and submission mechanism of a local, isolated HTCondor cluster highly available. The cluster consists of 2 master servers (previously 1) and several compute ...
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77 views

Using HPC managers like Slurm on multiple servers in LAN [closed]

I have access to a group of servers connected with a 1Gb LAN, and each of them has 40+ cores and Ubuntu OS. They all have a common NAS. I installed SLURM on a few of them and configured it so that ...
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What can be a reason for different clock speeds between sockets on 2 x Xeon Scalable 6148?

I have server with dual Xeon Scalable 6148 CPUs running HPC application. Base clock: 2.4GHz All core Turbo: 3.1 GHz Some processing threads are not scaling well and are sensitive to cpu clock. I ...
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183 views

Single-node SLURM server: restrict interactive CPU usage

I have SLURM setup on a single node, which is also a 'login node'. I would like to restrict interactive CPU usage, e.g. outside the scheduling system. I found the following article which suggests to ...
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216 views

Ubuntu server vs Ubuntu desktop for Beowulf cluster

I want to create a beowulf cluster using Ubuntu 18. Looking at some guides they all seem to use ubuntu server for this an my question is why? Is it not possible to use ubuntu desktop for the client ...
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How is it that Summit at Oak Ridge National Lab has 2,414,592 cores? [closed]

Top500 says that Summit has 2,414,592 cores: https://www.top500.org/system/179397. But they have 4608 nodes, 9216 chips (each node has 2 chips), and 22 cores per chip. This is 202,752 cores. Where ...
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303 views

What does “CPU Minutes” mean exactly?

I'm actually trying to report cluster utilization in Slurm but i don't understand the metric CPU Minutes. [root@XXXX]# sreport cluster Utilization Start=2018-12-01 End=2018-12-31 ---------------------...
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69 views

Exascale Power Consumption

I have read a lot of articles about exascale and found out that it may consumes approximately 20MW power envelope. Is it a daily basis or a yearly basis or every second? Please enlighten me. Here are ...
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629 views

Configure Singularity to do headless rendering / use OpenGL / glxgears / glxinfo

I want to do headless rendering on a server where I do not have root permissions. Therefore, I created a Singularity container like this: Bootstrap: docker From: nvidia/cuda:9.0-runtime-ubuntu16.04 %...
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2k views

Intel Xeon 6134 + One DIMM per channel or two DIMMs per channel for maximum memory bandwidth?

I'm unable to find this critical piece of information in spec sheets. Appreciate any insight. We're purchasing servers for HPC work with intel Xeon Gold 6134 (Skylake) cpus I want maximum memory ...
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1answer
86 views

Micosoft HPC Pack 2012 R2 does not run with Network Direct after joining new domain

I am working with a 13 computer cluster, running on Windows Server 2012 R2, using MS HPC Pack 2012 R2. The headnode is working properly. The servers are connected to the corporate network via IPv4 on ...
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34 views

Are processors more efficient at lower temperatures

I couldn't find a stackexchange site that's more suited for this question, I apologize. This doesn't necessarily have a lot to do with servers and stability.... I do not have problems with stability ...
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172 views

How to handle mpi head node failure?

There is app which starting with mpirun. If compute node fail then all processes crush, but if only head node fail(for example reboot) then processes will stuck on compute nodes. How to get rid of ...
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617 views

Randomize Slurm Node Allocation

Has anyone had luck randomizing Slurm node allocations? We have a small cluster of 12 nodes that could be used by anywhere from 1-8 people at a time with jobs of various size/length. When testing our ...
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346 views

MAAS for diskless computational hpc cluster

I'm considering to use MAAS to deploy OS for a computational cluster. All nodes are diskless. Only head node and (probably) MAAS rack controller will have hard drives. It seems MAAS have to finish a ...
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22 views

Ideal configuration for a head node? [duplicate]

Which hardware should I concentrate on, when assembling a head node for an HPC cluster? The main task for the head node is to relay instructions to the compute nodes which will be running artificial ...
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1answer
419 views

ifconfig apparently showing wrong RX/TX values for InfiniBand HCA

Recently, I executed a watch -n 1 ipconfig on one of our Linux cluster computing nodes while it was running a 48-process MPI run, disributed over several nodes. Oddly, while Ethernet packets seem to ...
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280 views

Containers for HPC batch processing

We are facing the problem that a lot of people want to run different scientific software on our high performance computing cluster. Every user requires a different set of libraries and library ...
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202 views

Solutions for monetizing excess CPU cycles [closed]

My company has a big (relatively) computer farm, say, 100 physical servers (dual CPU hexacore e5 xeons with 160 Gb RAM) leased from some hardware provider (say Leaseweb or OVM) on monthly basis, means,...
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1answer
93 views

How many infiniband adapters should be used in multi socket servers?

Should dual socket motherboards have an infinity band adapter for each CPU? That is, should there be two infiniband band adapters, one in each CPU's PCIe slot. Would this eliminate the signal going ...
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109 views

SSH vs qlogin to use all processors of a computing node

I have a SGE cluster consisting of four computing nodes, each with 20 processors. I do not mind to give one particular user the full capabilities of one specific node, i.e. I do not mind he/she uses ...
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126 views

memory usage per user in SGE cluster

I would like to automate the estimation of monthly memory usage of all jobs performed by a given user in my cluster (SGE, ubuntu). I have seen there are many tools to compute the current memory usage ...
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1answer
1k views

Slurm: Have two separate queues for GPU and CPU-only jobs

At the moment, we have set up Slurm to manage a small cluster of six nodes with four GPUs each. That has been working great so far, but now we want to utilize the Intel Core i7-5820K CPUs for jobs ...
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1answer
50 views

why all hard drives in a HPC cluster must be of the same size and part number? [closed]

One of the hard drives of my HPCC is broken and I have to buy another one. I've heard it must be of the exactly same size and part number. Could anyone explain me why? Thanks
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Torque queue issue

I am having troubles with Torque + Maui. The problem is the following: I have 2 queues, each queue has 10 associated nodes. If i submit 10k jobs to the first queue and i submit 1 job to the second ...
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208 views

Deployment of Base-Node via iSCSI in Server 2012R2 HPC cluster fails (can not join domain)

We are currently evaluating Server 2012R2 with HPC Pack for an upcoming project. Sadly we are stuck at deploying the base node. The node boots via PXE (iPXE) and connects to iSCSI, installs Windows ...
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1answer
195 views

deploying base note for HPC cluster in server 2012R2 hangs

We are in the process of evaluating server 2012R2 standard with HPC pack for a small cluster of nodes (about 40 to start with - the current setup has only one compute node). For the moment we use old ...
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Why does requesting GPUs as a generic resource on a cluster running SLURM with the built-in plugin fail?

Disclaimer: This post is quite long as I tried to provide all relevant configuration information. Status and Problem: I adminster a gpu cluster and I want to use slurm for job management. ...
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1answer
112 views

No service for subscription

I am trying to set up bursting to Azure with a Windows HPC cluster. THe cluster already works fine and I can start jobs on the machines on that are on the local network. When I try and create a node ...
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2answers
262 views

Why configure cluster nodes to reboot when out of memory?

I have access to a research HPC cluster which is configured so that if your job tries to use more memory than the node has available the node crashes and automatically reboots. This appears to be ...
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1answer
136 views

Parallel Processing and Disk IO for performance. More cores or more servers?

I have a large analysis job on an AWS EC2 instance (c3.8xlarge) on Ubuntu 12.04. The objective is to load the server at 100% CPU, running as many jobs as memory allows (varying amounts but generally ...
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1answer
1k views

Building Windows server cluster hpc

I'm trying to set up a Windows Server cluster with a head node and 2x compute nodes. So far, i've managed to install : (thanks to this tutorial http://msdn.microsoft.com/en-us/library/jj884142.aspx) ...
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1answer
3k views

HPC Cluster (SLURM): recommended ways to set up a secure and stable system

I'm working with a SLURM driven HPC Cluster, containing of 1 control node and 34 computation nodes and since the current system is not exactly very stable I'm looking for guidelines or best practices ...
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1answer
43 views

Parallel filesystem which schedules simultaneous file requests to mutually exclusive sets of OSSs

My environment is RHEL based, interconnect is infiniband. I have some experience with Lustre. What i want to know is: Is there a parallel file-system, where if simultaneous write request arrive, ...
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446 views

Windows VMs on ScaleMP cluster?

I was wondering whether the following stack would work, and if so then how well, and what sort of problems I might expect to encounter when setting it up? Hardware layer - lots of cheap servers SMP ...
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4k views

Numerous pbs_server errors in /var/log/messages

On supercomputer's management node we receive numerous errors such as: pbs_server: LOG_ERROR::is_request, bad attempt to connect from 10.10.0.254:1023 (address not trusted - check entry in ...
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1answer
227 views

HPC / EC2 - optimizing NFS for relialibility

In AWS-EC2, I've set-up a cluster of linux virtual machines made of an NFS fileserver and many clients. If the number of clients is above ~20, under heavy I/O, I am experiencing loss of file integrity:...
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1answer
81 views

Running jobs in a HPC cluster [closed]

I'm quite new to HPC environment. Is there any difference in running a job on a node utilizing 8 cores and running the same job on 8 nodes utilizing I core in terms of performance or walltime used. ...
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1answer
4k views

XFS Adding Quotas - Skip Quota check on first mount/boot

We run a 14TB XFS fileserver on our cluster and want to add quota support. This is running 3.9.2-1.el6.elrepo.x86_64 kernel under CentOS 6.3 (Final). The issue is when we unmount the XFS RAID, and re-...