Re: Failure to run namd-cuda with gtx-470

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Wed Jul 06 2011 - 16:18:53 CDT

Replying as the author:

Solved by setting persistent mode and monitoring from a ssh-linked
desktop. The gtx470 machine appears from its terminal (no X system was
raised) as if it were hanged (keyboard not sensed, terminal blinking
at a stage long before namd md had started), actually it is working
regularly (top -i: 6 processors; nvidia-smi -q - d TEMPERATURE output
90, 85), correct *.log. To avoid software problems to the gtx-470
machine, shutdown will have to be issued from the desktop. I wonder
whether there is a problem with nvidia latest driver using gtx470
(problems started from upgrading to latest driver), however i don't
mind as far as i can work. chiendarret

On Wed, Jul 6, 2011 at 5:44 PM, Francesco Pietra <chiendarret_at_gmail.com> wrote:
> While I could run namd-cuda md simulations without problems after
> running (as root)
>
> nvidia-smi -L
>
> the situation has gradually worsened. After a two-days successl
> simulation, this afternoon a similar simulation does not start at all
> and the computer does no more sense the keyboard, as if it were
> hanged. Actually, looking at /var/log/messages of the gig64 machine
> from a ssh-linked desktop, kernel problems are indicated, as reported
> in part below.
>
> ******************
> Jul  6 17:26:42 gig64 kernel: [  230.179942] NVRM: GPU at 0000:01:00.0
> has fallen off the bus.
> Jul  6 17:28:04 gig64 kernel: [  312.424094] Modules linked in:
> powernow_k8 mperf cpufreq_conservative cpufreq_powersave cpufreq_stats
> cpufreq_userspace fuse nfsd exportfs nfs lockd fscache nfs_acl
> auth_rpcgss sunrpc ext2 it87 hwmon_vid loop firewire_sbp2
> snd_hda_codec_hdmi nvidia(P) snd_hda_codec_realtek snd_hda_intel
> snd_hda_codec snd_hwdep snd_pcm snd_seq snd_timer snd_seq_device evdev
> pcspkr k10temp snd i2c_piix4 soundcore edac_core edac_mce_amd i2c_core
> parport_pc snd_page_alloc parport wmi button processor thermal_sys
> ext3 jbd mbcache dm_mod raid1 md_mod usbhid hid sg sr_mod sd_mod cdrom
> crc_t10dif ata_generic ohci_hcd xhci_hcd pata_atiixp pata_jmicron ahci
> libahci libata ehci_hcd firewire_ohci usbcore firewire_core scsi_mod
> crc_itu_t floppy nls_base r8169 mii [last unloaded: scsi_wait_scan]
> Jul  6 17:28:04 gig64 kernel: [  312.424204] CPU 4
> Jul  6 17:28:04 gig64 kernel: [  312.424208] Modules linked in:
> powernow_k8 mperf cpufreq_conservative cpufreq_powersave cpufreq_stats
> cpufreq_userspace fuse nfsd exportfs nfs lockd fscache nfs_acl
> auth_rpcgss sunrpc ext2 it87 hwmon_vid loop firewire_sbp2
> snd_hda_codec_hdmi nvidia(P) snd_hda_codec_realtek snd_hda_intel
> snd_hda_codec snd_hwdep snd_pcm snd_seq snd_timer snd_seq_device evdev
> pcspkr k10temp snd i2c_piix4 soundcore edac_core edac_mce_amd i2c_core
> parport_pc snd_page_alloc parport wmi button processor thermal_sys
> ext3 jbd mbcache dm_mod raid1 md_mod usbhid hid sg sr_mod sd_mod cdrom
> crc_t10dif ata_generic ohci_hcd xhci_hcd pata_atiixp pata_jmicron ahci
> libahci libata ehci_hcd firewire_ohci usbcore firewire_core scsi_mod
> crc_itu_t floppy nls_base r8169 mii [last unloaded: scsi_wait_scan]
> Jul  6 17:28:04 gig64 kernel: [  312.424302]
> Jul  6 17:28:04 gig64 kernel: [  312.424309] Pid: 2916, comm: namd2
> Tainted: P           O 2.6.38-2-amd64 #1 Gigabyte Technology Co., Ltd.
> GA-890FXA-UD5/GA-890FXA-UD5
> Jul  6 17:28:04 gig64 kernel: [  312.424322] RIP:
> 0010:[<ffffffffa07d4f74>]  [<ffffffffa07d4f74>]
> _nv015265rm+0x252/0x260 [nvidia]
> Jul  6 17:28:04 gig64 kernel: [  312.424951] RSP:
> 0018:ffff88042075fc88  EFLAGS: 00000297
> Jul  6 17:28:04 gig64 kernel: [  312.424958] RAX: 00000000ffffffff
> RBX: ffff88042b522000 RCX: 0000000000000019
> Jul  6 17:28:04 gig64 kernel: [  312.424964] RDX: 00000000ffffffff
> RSI: 0000000000005499 RDI: ffff88042b522028
> Jul  6 17:28:04 gig64 kernel: [  312.424971] RBP: ffff8804217f2c88
> R08: ffff8804217f2c98 R09: 0000000000000000
> Jul  6 17:28:04 gig64 kernel: [  312.424977] R10: 0000000000000246
> R11: 0000000000000028 R12: ffffffff8100a30e
> Jul  6 17:28:04 gig64 kernel: [  312.424983] R13: 0000000000000000
> R14: 0000000000000246 R15: 0000000000000028
> Jul  6 17:28:04 gig64 kernel: [  312.424991] FS:
> 00007f2f355a1720(0000) GS:ffff8800bfb00000(0000)
> knlGS:0000000000000000
> Jul  6 17:28:04 gig64 kernel: [  312.424998] CS:  0010 DS: 0000 ES:
> 0000 CR0: 000000008005003b
> Jul  6 17:28:04 gig64 kernel: [  312.425004] CR2: 00007f2f33947000
> CR3: 000000041ef84000 CR4: 00000000000006e0
> Jul  6 17:28:04 gig64 kernel: [  312.425010] DR0: 0000000000000000
> DR1: 0000000000000000 DR2: 0000000000000000
> Jul  6 17:28:04 gig64 kernel: [  312.425016] DR3: 0000000000000000
> DR6: 00000000ffff0ff0 DR7: 0000000000000400
> Jul  6 17:28:04 gig64 kernel: [  312.425024] Process namd2 (pid: 2916,
> threadinfo ffff88042075e000, task ffff88041e5cd7c0)
> Jul  6 17:28:04 gig64 kernel: [  312.425065]  ffff88042b522000
> 0000000000000045 0000000000000000 0000000000000003
> Jul  6 17:28:04 gig64 kernel: [  312.425077]  0000000000000000
> ffffffffa045b0dc ffff88042b522000 ffff88042b057000
> Jul  6 17:28:04 gig64 kernel: [  312.425088]  ffff88042fb30000
> ffffffffa045b2e1 0000000000000002 0000000000000003
> Jul  6 17:28:04 gig64 kernel: [  312.425494]  [<ffffffffa045b0dc>] ?
> _nv002890rm+0x8b/0x9c [nvidia]
> Jul  6 17:28:04 gig64 kernel: [  312.425853]  [<ffffffffa045b2e1>] ?
> _nv005068rm+0x1f4/0x20a [nvidia]
> Jul  6 17:28:04 gig64 kernel: [  312.426368]  [<ffffffffa069a5d7>] ?
> _nv010159rm+0x97b/0x9a9 [nvidia]
> Jul  6 17:28:04 gig64 kernel: [  312.426881]  [<ffffffffa069303a>] ?
> _nv010153rm+0x314/0x3eb [nvidia]
> Jul  6 17:28:04 gig64 kernel: [  312.427194]  [<ffffffffa03dc728>] ?
> _nv002567rm+0x8c6/0x9a8 [nvidia]
> Jul  6 17:28:04 gig64 kernel: [  312.427511]  [<ffffffffa03ebe35>] ?
> _nv002030rm+0xac/0xf0 [nvidia]
> Jul  6 17:28:04 gig64 kernel: [  312.427827]  [<ffffffffa03ebe00>] ?
> _nv002030rm+0x77/0xf0 [nvidia]
> Jul  6 17:28:04 gig64 kernel: [  312.428001]  [<ffffffffa0a20265>] ?
> _nv002424rm+0x5b5/0x751 [nvidia]
> Jul  6 17:28:04 gig64 kernel: [  312.428001]  [<ffffffffa0a1a8b1>] ?
> rm_ioctl+0x30/0x10a [nvidia]
> Jul  6 17:28:04 gig64 kernel: [  312.428001]  [<ffffffffa0a390e9>] ?
> nv_kern_ioctl+0x31a/0x381 [nvidia]
> Jul  6 17:28:04 gig64 kernel: [  312.428001]  [<ffffffffa0a3918d>] ?
> nv_kern_unlocked_ioctl+0x1c/0x20 [nvidia]
> Jul  6 17:28:04 gig64 kernel: [  312.428001]  [<ffffffff81104b0b>] ?
> do_vfs_ioctl+0x467/0x4b4
> Jul  6 17:28:04 gig64 kernel: [  312.428001]  [<ffffffff810d60fd>] ?
> do_brk+0x2ca/0x326
> Jul  6 17:28:04 gig64 kernel: [  312.428001]  [<ffffffff81104ba3>] ?
> sys_ioctl+0x4b/0x70
> Jul  6 17:28:04 gig64 kernel: [  312.428001]  [<ffffffff81009952>] ?
> system_call_fastpath+0x16/0x1b
> Jul  6 17:28:04 gig64 kernel: [  312.428001] Call Trace:
> Jul  6 17:28:04 gig64 kernel: [  312.428001]  [<ffffffffa045b0dc>] ?
> _nv002890rm+0x8b/0x9c [nvidia]
> Jul  6 17:28:04 gig64 kernel: [  312.428001]  [<ffffffffa045b2e1>] ?
> _nv005068rm+0x1f4/0x20a [nvidia]
> Jul  6 17:28:04 gig64 kernel: [  312.428001]  [<ffffffffa069a5d7>] ?
> _nv010159rm+0x97b/0x9a9 [nvidia]
> Jul  6 17:28:04 gig64 kernel: [  312.428001]  [<ffffffffa069303a>] ?
> _nv010153rm+0x314/0x3eb [nvidia]
> Jul  6 17:28:04 gig64 kernel: [  312.428001]  [<ffffffffa03dc728>] ?
> _nv002567rm+0x8c6/0x9a8 [nvidia]
> Jul  6 17:28:04 gig64 kernel: [  312.428001]  [<ffffffffa03ebe35>] ?
> _nv002030rm+0xac/0xf0 [nvidia]
> Jul  6 17:28:04 gig64 kernel: [  312.428001]  [<ffffffffa03ebe00>] ?
> _nv002030rm+0x77/0xf0 [nvidia]
> Jul  6 17:28:04 gig64 kernel: [  312.428001]  [<ffffffffa0a20265>] ?
> _nv002424rm+0x5b5/0x751 [nvidia]
> Jul  6 17:28:04 gig64 kernel: [  312.428001]  [<ffffffffa0a1a8b1>] ?
> rm_ioctl+0x30/0x10a [nvidia]
> Jul  6 17:28:04 gig64 kernel: [  312.428001]  [<ffffffffa0a390e9>] ?
> nv_kern_ioctl+0x31a/0x381 [nvidia]
> Jul  6 17:28:04 gig64 kernel: [  312.428001]  [<ffffffffa0a3918d>] ?
> nv_kern_unlocked_ioctl+0x1c/0x20 [nvidia]
> Jul  6 17:28:04 gig64 kernel: [  312.428001]  [<ffffffff81104b0b>] ?
> do_vfs_ioctl+0x467/0x4b4
> Jul  6 17:28:04 gig64 kernel: [  312.428001]  [<ffffffff810d60fd>] ?
> do_brk+0x2ca/0x326
> Jul  6 17:28:04 gig64 kernel: [  312.428001]  [<ffffffff81104ba3>] ?
> sys_ioctl+0x4b/0x70
> Jul  6 17:28:04 gig64 kernel: [  312.428001]  [<ffffffff81009952>] ?
> system_call_fastpath+0x16/0x1b
> root_at_gig64:/var/log#
> Message from syslogd_at_gig64 at Jul  6 17:29:28 ...
>  kernel:[  396.424694] Stack:
>
> Message from syslogd_at_gig64 at Jul  6 17:29:28 ...
>  kernel:[  396.424762] Call Trace:
>
> Message from syslogd_at_gig64 at Jul  6 17:29:28 ...
>  kernel:[  396.428001] Code: be a0 e8 85 65 60 00 b8 00 00 00 00 e8 9d
> 65 60 00 85 c0 74 10 e8 84 28 63 00 0f 1f 00 eb 06 89 77 68 89 4f 6c
> 48 83 c5 10 5b c3 <41> 54 53 48 83 ec 08 48 83 ed 08 41 89 f4 39 77 68
> 73 17 39 77
> ******************
>
> such messages from syslog_at_gig64 continue at slow pace.
>
>
> Thanks for advice
>
> francesco pietra
>
>

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