*** Error in `python': corrupted size vs. prev_size: 0x000056364f396870 ***
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ema...@iastate.edu
Feb 8, 2022, 12:41:36 PM2/8/22
to hoomd-users
Hello,
I have created an environment that uses python 3.10.2. I also, install HOOMD with force GPU installation by typing the command line,
$ conda install -c conda-forge hoomd=*=*gpu*
When I try to run a program, I get this error:
*** Error in `python': corrupted size vs. prev_size: 0x000056364f396870 ***
Is this related to the forced GPU installation? I have an environment that does not have forced GPU installation, runs HOOMD with CPU (and Python 3.9.10), and I do not get this error.
Thank you,
Elizabeth
Elizabeth Macias
Feb 8, 2022, 1:04:57 PM2/8/22
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Running with the same python (3.9) does not make a difference.
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Elizabeth Macias
Feb 8, 2022, 1:51:05 PM2/8/22
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So I am getting a runtime error when I use the GPU forced installation.
Elizabeth Macias
Feb 8, 2022, 1:57:54 PM2/8/22
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So, I get this error when I run a program in the environment with python 3.9 while I have another environment with python 3.10.2. When I delete the environment with python 3.10.2, I no longer get this error message.
Elizabeth Macias
Elizabeth Macias
Feb 8, 2022, 1:58:18 PM2/8/22
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However, I do get a runtime error.
Elizabeth Macias
Feb 8, 2022, 2:17:53 PM2/8/22
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Actuall,
I still get the error: *** Error in `python': corrupted size vs. prev_size: 0x000056364f396870 ***
Joshua Anderson
Feb 9, 2022, 7:58:53 AM2/9/22
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Elizabeth,
Please don't spam the list. Every message you send goes out to 700+ list members. You could have sent 1 message describing the problem instead of 7.
Please also take the time to clearly describe the steps that you take and include the platform you are using, the specific versions of HOOMD that you install, the input command, the expected output, and copy and paste the actual output you get.
I am unable to reproduce any of the behavior you describe. I do not get the "corrupted size" error, nor do I get a "runtime error".
To test, I installed a fresh copy of miniforge x86_64 (amd64) from https://github.com/conda-forge/miniforge on my Arch Linux workstation. Then I upgraded to python 3.10, installed HOOMD, verified the package versions, and tested HOOMD. See the commands and output below.
$ conda install python=3.10
$ conda install hoomd
$ conda list hoomd
# Name Version Build Channel
hoomd 2.9.7 cpu_py310he3ee615_1 conda-forge
$ python3
Python 3.10.2 | packaged by conda-forge | (main, Feb 1 2022, 19:28:35) [GCC 9.4.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import hoomd
>>> hoomd.context.initialize()
HOOMD-blue 2.9.7 DOUBLE HPMC_MIXED TBB SSE SSE2 SSE3
Compiled: 11/08/2021
Copyright (c) 2009-2019 The Regents of the University of Michigan.
-----
You are using HOOMD-blue. Please cite the following:
* J A Anderson, J Glaser, and S C Glotzer. "HOOMD-blue: A Python package for
high-performance molecular dynamics and hard particle Monte Carlo
simulations", Computational Materials Science 173 (2020) 109363
-----
HOOMD-blue is running on the CPU
<hoomd.context.SimulationContext object at 0x7ff6d3e5b130>
>>>
For the GPU:
$ conda install "hoomd=*=*gpu*"
$ conda list hoomd
# Name Version Build Channel
hoomd 2.9.7 gpu_py310h1718d14_1 conda-forge
$ python3
Python 3.10.2 | packaged by conda-forge | (main, Feb 1 2022, 19:28:35) [GCC 9.4.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import hoomd
>>> hoomd.context.initialize()
HOOMD-blue 2.9.7 CUDA (11.2) DOUBLE HPMC_MIXED TBB SSE SSE2 SSE3
Compiled: 11/08/2021
Copyright (c) 2009-2019 The Regents of the University of Michigan.
-----
You are using HOOMD-blue. Please cite the following:
* J A Anderson, J Glaser, and S C Glotzer. "HOOMD-blue: A Python package for
high-performance molecular dynamics and hard particle Monte Carlo
simulations", Computational Materials Science 173 (2020) 109363
-----
HOOMD-blue is running on the following GPU(s):
[0] Quadro RTX 5000 48 SM_7.5 @ 1.82 GHz, 16124 MiB DRAM, DIS, MNG
<hoomd.context.SimulationContext object at 0x7f89631e3400>
>>>
------
Joshua A. Anderson, Ph.D.
Research Area Specialist, Chemical Engineering, University of Michigan
> You received this message because you are subscribed to the Google Groups "hoomd-users" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to hoomd-users...@googlegroups.com.
> To view this discussion on the web visit https://groups.google.com/d/msgid/hoomd-users/CAPRcbrGp7DC2M2pB9LqC806mL7VM0WGZ%2BqcetiTSizutYfvT8g%40mail.gmail.com.
Please don't spam the list. Every message you send goes out to 700+ list members. You could have sent 1 message describing the problem instead of 7.
Please also take the time to clearly describe the steps that you take and include the platform you are using, the specific versions of HOOMD that you install, the input command, the expected output, and copy and paste the actual output you get.
I am unable to reproduce any of the behavior you describe. I do not get the "corrupted size" error, nor do I get a "runtime error".
To test, I installed a fresh copy of miniforge x86_64 (amd64) from https://github.com/conda-forge/miniforge on my Arch Linux workstation. Then I upgraded to python 3.10, installed HOOMD, verified the package versions, and tested HOOMD. See the commands and output below.
$ conda install python=3.10
$ conda install hoomd
$ conda list hoomd
# Name Version Build Channel
hoomd 2.9.7 cpu_py310he3ee615_1 conda-forge
$ python3
Python 3.10.2 | packaged by conda-forge | (main, Feb 1 2022, 19:28:35) [GCC 9.4.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import hoomd
>>> hoomd.context.initialize()
HOOMD-blue 2.9.7 DOUBLE HPMC_MIXED TBB SSE SSE2 SSE3
Compiled: 11/08/2021
Copyright (c) 2009-2019 The Regents of the University of Michigan.
-----
You are using HOOMD-blue. Please cite the following:
* J A Anderson, J Glaser, and S C Glotzer. "HOOMD-blue: A Python package for
high-performance molecular dynamics and hard particle Monte Carlo
simulations", Computational Materials Science 173 (2020) 109363
-----
HOOMD-blue is running on the CPU
<hoomd.context.SimulationContext object at 0x7ff6d3e5b130>
>>>
For the GPU:
$ conda install "hoomd=*=*gpu*"
$ conda list hoomd
# Name Version Build Channel
hoomd 2.9.7 gpu_py310h1718d14_1 conda-forge
$ python3
Python 3.10.2 | packaged by conda-forge | (main, Feb 1 2022, 19:28:35) [GCC 9.4.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import hoomd
>>> hoomd.context.initialize()
HOOMD-blue 2.9.7 CUDA (11.2) DOUBLE HPMC_MIXED TBB SSE SSE2 SSE3
Compiled: 11/08/2021
Copyright (c) 2009-2019 The Regents of the University of Michigan.
-----
You are using HOOMD-blue. Please cite the following:
* J A Anderson, J Glaser, and S C Glotzer. "HOOMD-blue: A Python package for
high-performance molecular dynamics and hard particle Monte Carlo
simulations", Computational Materials Science 173 (2020) 109363
-----
HOOMD-blue is running on the following GPU(s):
[0] Quadro RTX 5000 48 SM_7.5 @ 1.82 GHz, 16124 MiB DRAM, DIS, MNG
<hoomd.context.SimulationContext object at 0x7f89631e3400>
>>>
------
Joshua A. Anderson, Ph.D.
Research Area Specialist, Chemical Engineering, University of Michigan
> To unsubscribe from this group and stop receiving emails from it, send an email to hoomd-users...@googlegroups.com.
> To view this discussion on the web visit https://groups.google.com/d/msgid/hoomd-users/CAPRcbrGp7DC2M2pB9LqC806mL7VM0WGZ%2BqcetiTSizutYfvT8g%40mail.gmail.com.
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