From: David Hardy (dhardy_at_ks.uiuc.edu)
Date: Wed Mar 07 2018 - 10:51:44 CST
Hi Mahmood,
It looks like you are building from the NAMD 2.12 released source back in Dec 2016.
Unfortunately, the new CUDA kernels released at that time introduced a bug in which MSM was not getting properly initialized, hence the seg fault you are seeing. The bug was discovered and fixed around March 2017.
See this earlier namd-l thread regarding the problem (and there are others):
http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2017-2018/0747.html <http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2017-2018/0747.html>
Since you are building NAMD, why not use an up-to-date version of the source? You can get it with this command:
git clone https://charm.cs.illinois.edu/gerrit/namd.git
(Besides which, support for CUDA 9 was not even possible back in 2016.)
See http://www.ks.uiuc.edu/Research/namd/development.html <http://www.ks.uiuc.edu/Research/namd/development.html> for more details on building NAMD.
Best regards,
Dave
-- David J. Hardy, Ph.D. Beckman Institute University of Illinois at Urbana-Champaign 405 N. Mathews Ave., Urbana, IL 61801 dhardy_at_ks.uiuc.edu, http://www.ks.uiuc.edu/~dhardy/ > On Mar 7, 2018, at 9:48 AM, Mahmood Naderan <mahmood.nt_at_gmail.com> wrote: > > Joshua, > As you can see below, the driver and smi versions are the same > > mahmood_at_orca:~$ nvidia-smi > Wed Mar 7 19:15:13 2018 > +-----------------------------------------------------------------------------+ > | NVIDIA-SMI 384.81 Driver Version: 384.81 | > |-------------------------------+----------------------+----------------------+ > | GPU Name Persistence-M| Bus-Id Disp.A | Volatile Uncorr. ECC | > | Fan Temp Perf Pwr:Usage/Cap| Memory-Usage | GPU-Util Compute M. | > |===============================+======================+======================| > | 0 Quadro M2000 Off | 00000000:23:00.0 On | N/A | > | 56% 40C P0 24W / 75W | 230MiB / 4035MiB | 3% Default | > +-------------------------------+----------------------+----------------------+ > > +-----------------------------------------------------------------------------+ > | Processes: GPU Memory | > | GPU PID Type Process name Usage | > |=============================================================================| > | 0 1144 G /usr/lib/xorg/Xorg 129MiB | > | 0 1627 G compiz 98MiB | > +-----------------------------------------------------------------------------+ > mahmood_at_orca:~$ nvcc --version > nvcc: NVIDIA (R) Cuda compiler driver > Copyright (c) 2005-2017 NVIDIA Corporation > Built on Fri_Sep__1_21:08:03_CDT_2017 > Cuda compilation tools, release 9.0, V9.0.176 > > > > > Any more idea? > > Regards, > Mahmood > > > > > On Wed, Mar 7, 2018 at 11:03 AM, Mahmood Naderan <mahmood.nt_at_gmail.com> wrote: >> The OS is Ubuntu and I installed the cuda-9 driver which comes from >> the toolkit package. The installation was successful and I can work >> with the nvccc, and other things. For example, the Nvidia X server >> setting window correctly shows the device, utilization, temperature >> and other things. >> >> Your sentence that the driver version must match smi version is not >> clear for me. Can you explain more? In what situations they might be >> different? >> >> Regards, >> Mahmood >>
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