Questions tagged [supercomputers]

Supercomputers belong to a class of highly specialised hardware infrastructures, where high number of machines are typically pre-organised and smart-linked together with specialised high-speed low-latency interconnects, so as to allow new forms of concurrent processing cooperations to be orchestrated. Having any such supercomputing infrastructure is not enough, it is important to also use system tools capable to harness the most of the available CPU-powers

Supercomputers first began to appear in the 1960's.

These early supercomputers had only a single, high-speed processor. Control Data Corporation's CDC-6600, designed by Seymour Cray, was about ten times faster than all other computers of its day, and was dubbed a supercomputer -- the first appearance of the term.

Later, as processing speed, cooling ability, and physical size hit limits, Cray pioneered the method of linking multiple processors together in order to get more speed out of the same machine. This is the same method used in today's supercomputers, which can range in size from thousands of processing cores to hundreds of thousands of processing cores.

*  Seymour CRAY (                           yes, the supercomputer guy )
*  said:
*  --------------------------------------------------------------------
*  A supercomputer turns compute-bound problems into I/O bound problems
*  --------------------------------------------------------------------
*  and:
*  --------------------------------------------------------------------
*  It is not hard to build a fast processor or a fast memory,
*  but the challenge is to build a fast system.
*  --------------------------------------------------------------------

Interconnect latency is an additional [TIME]-domain penalty, each process has to pay for using a supercomputer's remote resource under a distributed computation-graph schedule.

Minimising interconnect's latency-costs is thus one natural direction, using a smarter, overhead-aware computation-graph design is the other direction to achieve the indeed I/O-bounds' bleeding edge of the ultimate performance from any supercomputing system's infrastructure.

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Is there any way to know which job will start next in qsub

In our institute (IISc Bangalore)Supercomputer ,we submit jobs using qsub. The jobs will start running according to the following- (1) Its wall time(Expected completion time) (2) Its position in the respected queue(small,medium,large etc). So,it is…
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Multiple processing using python to run scripts on a super computer

I am trying to run two python scripts as described below. This code is designed to download data from a specific URL of the file. years = ["2013","2014","2018","2019"] for year in years: code(year) In this case, code is the downloading function. I…
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how to make separate temp directories for each processes in a batch job

I have just started learning bioinformatics in my lab and I am a complete newbie. I am using a genome annotation tool called Kofamscan from NCBI and I am getting an error that could be due to the fact results of multiple processes are being stored…
Ryohei
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How to make a clustercomputer testcode with python? (RPI)

I made a clustercomputer for a school project. Only i am having some problems with making a code that uses all eight Raspberry pi's. https://www.instructables.com/id/How-to-Make-a-Raspberry-Pi-SuperComputer/ This is the base i used to make…
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how to send a bash command to command line using python and execute next command without waiting for bash command to execute?

I want to execute a 3 separate bash commands on 3 separate core processors of a node of a supercomputer. I have a python script that sends a bash command via os.system to the command line, however it seems to execute the bash command to completion…
user4991878
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Python: IOError 110 Connection timed out when reading from disk

I'm running a Python script on a Sun Grid Engine supercompute cluster that reads in a list of file ids, sends each to a worker process for analysis, and writes one output per input file to disk. The trouble is I'm getting IOError(110, 'Connection…
duhaime
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Performance of MPI_Reduce vs (MPI_Gather + Reduction on Root)

CRAY supercomputer using the MPICH2 library. Each node has 32 CPU's. I have a single float on N different MPI ranks, where each of these ranks is on a different node. I need to perform a reduction operation on this group of floats. I would like to…
wiowou
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parallel processing: class file has wrong version 49.0, should be 48.0

I run my code in supercomputer by used terminal. I have 2 kind of code: 1- sequential and parallel (shared memory) the sequential one it run correctly, but when I run the SM I have this error when I enter th command javac : mycode.java:7: cannot…
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fortran: relocation truncated to fit, i can't create big arrays on server

I write a simple subroutine in fortran for a more complicated program. I need to read a file containing 3 columns of numbers (X_halo, Y_halo, Z_halo) and enter the 3 columns data into 3 arrays. In this subroutine I write the data in a file to see…
Alessandro Peca
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Loop through all files in a directory simultaneously

I have a a loop within a loop The outer loop just goes through each file in a directory and runs the inner loop Can I select multiple files and have the inner loop running on these files simultaneously I am using a 32 core 100gb ram server. And I…
Lucas
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How to run normal program in mpich clusters?

I'm making a cluster network(kind of super computer, but 'super fast') with my ubuntu installed computers, to run mprime of GIMPS Project. I used this tutorial. However, I don't know how to run mprime in my clusters. mpi exec -n 4 -f…
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How do I save output from a large simulation in R? (multiple nodes, safe access)

I am doing a large simulation for a research project--simulating 1,000 football seasons and analyzing the results. As the seasons will be spread across multiple nodes, I need an easy way to save my output data into a file (or files) to access later.…
jntrcs
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Submitting jobs in parallel

I want to analyze data from different files (let's say 10) which are not related to each other. I want to know what is the difference between submitting the jobs in parallel or opening 10 terminals and submitting the job 10 times. I want to know the…
Silviu
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signal 11 in a linux shell remote site. How can I troubleshoot

I'm a bio major only recently doing major coding for research stuff. Our campus in order to support research has an on campus supercomputer for researcher use. I work remotely from this supercomputer and it uses a linux shell to access it and submit…
addiseg
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How to see the current user's queue in SLURM

On a cluster that is managed by SLURM, I want to check the queue of the current user (and cluster). Normally, I have to use this command: squeue --user=username --clusters=clustername The problem with this, apart from the fact that this is a rather…
MakisH
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