[PVFS-users] pvfs 1.6.3 causing possible kernel crash
Shawn Needham
shawn at flash.uchicago.edu
Tue Dec 21 13:06:59 EST 2004
Hi Rob,
On Tue, 21 Dec 2004, Rob Ross wrote:
> Hi Shawn,
>
> Can you send us the configure output from the pvfs-kernel build? I'd like
> to know what options it picked.
I've attached the log from the pvfs-1.6.3-kernel-2.4 build. If you need
more than this let me know.
>
> Also, when you load the module, are you specifying a specific "buffer="
> argument? If you could grab the line out of dmesg that is printed at
> module load time, that would be helpful.
Rob, I didn't set any special buffer argument. I'm just relying on the
default setting for that argument which is to handle it dynamically. I'm
guessing that setting this statically could greatly change it's
stability/performance. Could let me know a good size to set this
buffer to for our configuration.
Dec 21 11:38:33 ellipse2 kernel: pvfs: debug = 0x0, maxsz = 16777216
bytes, buffer = dynamic, major = 0
>
> If this is a PVFS problem, it is most likely in the kernel code; otherwise
> you shouldn't get hangs.
>
> I don't understand why you're getting much traffic at all across the
> kernel interface with the FLASH code; I think that it is likely that
> something is misconfigured there in the I/O stack. Can you try prepending
> a "pvfs:" to your file names and see if that helps? Alternatively, you
> could create an /etc/pvfstab describing the mount point and not mount the
> file system at all, eliminating the pvfs-kernel piece from the equation
> entirely.
I have created the /etc/pvfstab entry for the mount point. So applications
should be able to interface with the filesystem without being mounted.
However, without having the kernel loaded and the client running is there
a way to access those directories with standard Linux commands (ls, cp,
etc). For testing not mounting these directories would be fine, but I'm
not sure it would offer an ideal situation down the road where user's
would want access to there data while running. I guess the latter point is
just something to keep in mind for now.
Thanks,
Shawn
>
> Rob
>
>
> On Mon, 20 Dec 2004, Shawn Needham wrote:
>
> > Greetings,
> >
> > In the past week I have been attempting to run our FLASH application on
> > our cluster using pvfs-1.6.3.
> >
> > We have been experiencing crashes on one of our compute nodes that
> > appears to be caused by software with direct access to the kernel. The
> > nodes are freezing, you can no longer ping the interface for the Gb
> > switch, the terminal is blacked out and unresponsive to keyboard input,
> > and no diagnostic information is written to the log files. The only 2
> > modules loaded on our compute nodes are gm (for a Myrinet's MPICH-gm)
> > and pvfs, which we are running as a service over the Gb switch.
> >
> > We have seen the crash occur with the exact same symptoms when trying to
> > run our application on a purely Gb based configuration (mpich/hdf5 p4
> > configuration and pvfs running over Gb based switch) and with the mixed
> > configuration described above. Actually the pure Gb configuration has
> > performed much worse and the crashes have always happened much quicker
> > in terms the amount of progress in our runs. Some of the Myrinet runs
> > have run to completion (though this hasn't been consistent when trying
> > the exact same run), but I never had any success with the Gb based runs
> > during which neither Myrinet did not have any services running and it's
> > module was not loaded.
> >
> > I was wondering if you have heard of pvfs causing problems similar to
> > these. Also if one of the developers would like to have an account on
> > the machine to investigate this further that would be tremendous. I have
> > been working with developers at Myrinet for the past week and their
> > ability to log on has proved beneficial. I'm open to trying pvfs2 if the
> > kernel module is more robust than pvfs-1.6.3 but would like to at least
> > get your insights into the current problem we are having with this
> > installation.
> >
> > I'm not sure if this relevant, but on two of our earliest runs some
> > corrupted file were produced right before our runs crashed. These files
> > were written to directories in the pvfs file system.
> >
> > I just reinstalled a new kernel this afternoon and rebuilt all the
> > software, scrapped all old pvfs directories and rebuilt them and my
> > Myrinet based run ended up dieing in the same manner as the others.
> >
> > I've also appending some information about the hardware/software
> > configuration of our machine.
> >
> > Thanks,
> > Shawn
> >
> > Here's the software/hardware information.
> >
> > Hardware. 17 node (1 master/16 compute) cluster from Aspen Systems with
> > the Myrinet M3-E32 switch and a Gb switch (24 port HP Procurve 2724,
> > J4897a).
> > Nodes: e7505 chipset, dual 2.8Ghz xeon processors 4GB memory. PCIXE-2
> > dual channel myrinet cards, cards are in 133Mhz PCI slots, Intel Corp.
> > 82545EM Gigabit Ethernet Controller. Nvidia 5950 Geforce FX Ultra.
> >
> > We are running a stock 2.4.27 kernel from kernel.org. The current
> > running kernel is a 2.4.27smp-64GB-noAGPsupport. We initially installed
> > RH9 on this system and tried to take as much of the RedHat features out
> > as possible, but system parameters are still consistent with RH values.
> > Here's /proc/version info.
> >
> > [root at ellipse0 ~]# cat /proc/version
> > Linux version 2.4.27smp-64gb-noagp (root at ellipse0) (gcc version 3.2.2
> > 20030222 (Red Hat Linux 3.2.2-5)) #1 SMP Mon Dec 20 12:14:14 CST 2004
> >
> > Myrinet configuration
> >
> > gm-2.1.6 (linux-2.4 - ia32)
> > pvfs-1.6.3 (running over Gb switch)
> > mpich-1.2.6..13b-gm * ifc 8.1 (Version 8.1 (l_fc_p_8.1.018))
> > * icc 8.1 (Version 8.1 (l_cc_p_8.1.021))
> > hdf5-1.6.2 (built against this mpich)
> >
> > Gb configuration (all services running over Gb based switch):
> >
> > pvfs-1.6.3
> > mpich-1.2.6-p4
> > ifc 8.1 (Version 8.1 Build 20040803Z Package ID:
> > l_fc_p_8.1.018)
> > gcc 3.2.2 (gcc (GCC) 3.2.2 20030222 (Red Hat Linux 3.2.2-5))
> > hdf5-1.6.2-p4 (built against mpich-1.2.6-p4)
> >
> > I have configured both MPICH libraries with-romio filesupport for the
> > following file systems (pvfs,ufs,nfs)
> >
> >
> > _______________________________________________
> > PVFS-users mailing list
> > PVFS-users at www.beowulf-underground.org
> > http://www.beowulf-underground.org/mailman/listinfo/pvfs-users
> >
> >
>
-------------- next part --------------
This file contains any messages produced by compilers while
running configure, to aid debugging if configure makes a mistake.
It was created by configure, which was
generated by GNU Autoconf 2.52. Invocation command line was
$ ./configure --with-pvfs=/usr/local/pvfs/pvfs-1.6.3
## ---------- ##
## Platform. ##
## ---------- ##
hostname = ellipse0
uname -m = i686
uname -r = 2.4.27smp-64gb-noagp
uname -s = Linux
uname -v = #1 SMP Mon Dec 20 12:14:14 CST 2004
/usr/bin/uname -p = unknown
/bin/uname -X = unknown
/bin/arch = i686
/usr/bin/arch -k = unknown
/usr/convex/getsysinfo = unknown
hostinfo = unknown
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/bin/universe = unknown
PATH = /usr/local/sbin:/usr/sbin:/sbin:/opt/intel_fc_80/bin:/opt/intel_cc_80/bin:/usr/local/sbin:/usr/local/bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/X11R6/bin:/usr/local/mpich-gm/bin:/usr/local/hdf5-1.6.2-gm/bin:/root/bin
## ------------ ##
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## ------------ ##
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gcc (GCC) 3.2.2 20030222 (Red Hat Linux 3.2.2-5)
Copyright (C) 2002 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
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In file included from configure:3662:
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int
main ()
{
int foo() { return 0; }
;
return 0;
}
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configure:3879: test -s conftest.o
configure:3882: $? = 0
configure:3910: gcc -o conftest -I/lib/modules/2.4.27smp-64gb-noagp/build/include -I/lib/modules/2.4.27smp-64gb-noagp/build/include -L/usr/local/pvfs/pvfs-1.6.3/lib conftest.c -lminipvfs -lminipvfs >&5
configure:3913: $? = 0
configure:3915: ./conftest
configure:3918: $? = 0
configure:3921: result: yes (SMP)
configure:3950: checking for modversions
configure:3977: gcc -c -I/lib/modules/2.4.27smp-64gb-noagp/build/include -I/lib/modules/2.4.27smp-64gb-noagp/build/include conftest.c >&5
configure:3980: $? = 0
configure:3983: test -s conftest.o
configure:3986: $? = 0
configure:4016: gcc -o conftest -I/lib/modules/2.4.27smp-64gb-noagp/build/include -I/lib/modules/2.4.27smp-64gb-noagp/build/include -L/usr/local/pvfs/pvfs-1.6.3/lib conftest.c -lminipvfs -lminipvfs >&5
configure:4019: $? = 0
configure:4021: ./conftest
configure:4024: $? = 0
configure:4027: result: yes
configure:4056: checking for highmem
configure:4083: gcc -c -I/lib/modules/2.4.27smp-64gb-noagp/build/include -I/lib/modules/2.4.27smp-64gb-noagp/build/include conftest.c >&5
configure:4086: $? = 0
configure:4089: test -s conftest.o
configure:4092: $? = 0
configure:4122: gcc -o conftest -I/lib/modules/2.4.27smp-64gb-noagp/build/include -I/lib/modules/2.4.27smp-64gb-noagp/build/include -L/usr/local/pvfs/pvfs-1.6.3/lib conftest.c -lminipvfs -lminipvfs >&5
configure:4125: $? = 0
configure:4127: ./conftest
configure:4130: $? = 0
configure:4133: result: yes
configure:4162: checking for devfs
configure:4189: gcc -c -I/lib/modules/2.4.27smp-64gb-noagp/build/include -I/lib/modules/2.4.27smp-64gb-noagp/build/include conftest.c >&5
configure:4192: $? = 0
configure:4195: test -s conftest.o
configure:4198: $? = 0
configure:4228: gcc -o conftest -I/lib/modules/2.4.27smp-64gb-noagp/build/include -I/lib/modules/2.4.27smp-64gb-noagp/build/include -L/usr/local/pvfs/pvfs-1.6.3/lib conftest.c -lminipvfs -lminipvfs >&5
configure:4231: $? = 0
configure:4233: ./conftest
configure:4236: $? = 1
configure: program exited with status 1
configure: failed program was:
#line 4209 "configure"
#include "confdefs.h"
#define __KERNEL__
#include <linux/config.h>
#include <linux/version.h>
#include <linux/module.h>
int main(void)
{
#if defined(CONFIG_DEVFS_FS)
return 0; /* true */
#else
return 1; /* false */
#endif
}
configure:4251: result: no
configure:4268: checking for s_maxbytes member in struct super_block
configure:4289: gcc -c -I/lib/modules/2.4.27smp-64gb-noagp/build/include -I/lib/modules/2.4.27smp-64gb-noagp/build/include conftest.c >&5
configure:4292: $? = 0
configure:4295: test -s conftest.o
configure:4298: $? = 0
configure:4300: result: yes
configure:4317: checking for deprecated linux/malloc.h
configure:4335: gcc -c -I/lib/modules/2.4.27smp-64gb-noagp/build/include -Werror -I/lib/modules/2.4.27smp-64gb-noagp/build/include conftest.c >&5
In file included from configure:4323:
/lib/modules/2.4.27smp-64gb-noagp/build/include/linux/malloc.h:4:2: #warning linux/malloc.h is deprecated, use linux/slab.h instead.
configure:4338: $? = 1
configure: failed program was:
#line 4320 "configure"
#include "confdefs.h"
#define __KERNEL__
#include <linux/malloc.h>
int
main ()
{
;
return 0;
}
configure:4351: result: yes
configure:4362: checking for alloc_kiovec_sz function
configure:4383: gcc -c -I/lib/modules/2.4.27smp-64gb-noagp/build/include -I/lib/modules/2.4.27smp-64gb-noagp/build/include conftest.c >&5
configure: In function `main':
configure:4375: `alloc_kiovec_sz' undeclared (first use in this function)
configure:4375: (Each undeclared identifier is reported only once
configure:4375: for each function it appears in.)
configure:4386: $? = 1
configure: failed program was:
#line 4365 "configure"
#include "confdefs.h"
#define __KERNEL__
#include <linux/iobuf.h>
int
main ()
{
int (*test_function)(int, struct kiobuf**, int*);
test_function = alloc_kiovec_sz;
;
return 0;
}
configure:4404: result: no
configure:4409: checking for sighand member of task_struct
configure:4429: gcc -c -I/lib/modules/2.4.27smp-64gb-noagp/build/include -I/lib/modules/2.4.27smp-64gb-noagp/build/include conftest.c >&5
configure: In function `main':
configure:4421: structure has no member named `sighand'
configure:4432: $? = 1
configure: failed program was:
#line 4412 "configure"
#include "confdefs.h"
#define __KERNEL__
#include <linux/sched.h>
int
main ()
{
spin_lock_irq(¤t->sighand->siglock);
;
return 0;
}
configure:4450: result: no
configure:4456: checking for for_each_process function
configure:4478: gcc -c -I/lib/modules/2.4.27smp-64gb-noagp/build/include -I/lib/modules/2.4.27smp-64gb-noagp/build/include conftest.c >&5
configure:4469:18: #error
configure:4481: $? = 1
configure: failed program was:
#line 4459 "configure"
#include "confdefs.h"
#define __KERNEL__
#include <linux/sched.h>
int
main ()
{
#ifndef for_each_process
#error
#endif
;
return 0;
}
configure:4499: result: no
configure:4507: checking for running kernel version match
configure:4518: result: yes (2.4)
configure:4529: checking for running kernel SMP settings match
configure:4541: result: yes (SMP)
configure:4554: checking for running kernel modversions match
configure:4567: result: yes (modversions on)
configure:4580: checking for running kernel highmem match
configure:4594: result: yes (highmem on)
configure:4608: checking for running kernel devfs match
configure:4624: result: yes (devfs off)
configure:4733: creating ./config.status
## ----------------------- ##
## Running config.status. ##
## ----------------------- ##
This file was extended by config.status 2.52, executed with
CONFIG_FILES =
CONFIG_HEADERS =
CONFIG_LINKS =
CONFIG_COMMANDS =
> ./config.status
on ellipse0
config.status:5196: creating test/Makefile
config.status:5196: creating Makefile
config.status:5196: creating libkpvfs/Makefile
config.status:5196: creating libkpvfs/klib/Makefile
config.status:5196: creating libkpvfs/kinclude/Makefile
config.status:5196: creating libkpvfs/kshared/Makefile
config.status:5196: creating libkernsys/Makefile
config.status:5288: creating config.h
## ----------------- ##
## Cache variables. ##
## ----------------- ##
ac_cv_build=i686-pc-linux-gnu
ac_cv_build_alias=i686-pc-linux-gnu
ac_cv_c_compiler_gnu=yes
ac_cv_c_const=yes
ac_cv_c_inline=inline
ac_cv_env_CC_set=
ac_cv_env_CC_value=
ac_cv_env_CFLAGS_set=
ac_cv_env_CFLAGS_value=
ac_cv_env_CPPFLAGS_set=
ac_cv_env_CPPFLAGS_value=
ac_cv_env_CPP_set=
ac_cv_env_CPP_value=
ac_cv_env_LDFLAGS_set=
ac_cv_env_LDFLAGS_value=
ac_cv_env_build_alias_set=
ac_cv_env_build_alias_value=
ac_cv_env_host_alias_set=
ac_cv_env_host_alias_value=
ac_cv_env_target_alias_set=
ac_cv_env_target_alias_value=
ac_cv_func_select=yes
ac_cv_header_fcntl_h=yes
ac_cv_header_inttypes_h=yes
ac_cv_header_linux_highmem_h=yes
ac_cv_header_linux_init_h=yes
ac_cv_header_linux_locks_h=yes
ac_cv_header_linux_malloc_h=yes
ac_cv_header_linux_modversions_h=yes
ac_cv_header_linux_pagemap_h=yes
ac_cv_header_linux_posix_types_h=yes
ac_cv_header_linux_seq_file_h=yes
ac_cv_header_linux_slab_h=yes
ac_cv_header_linux_smp_lock_h=yes
ac_cv_header_linux_tqueue_h=yes
ac_cv_header_linux_vmalloc_h=yes
ac_cv_header_malloc_h=yes
ac_cv_header_memory_h=yes
ac_cv_header_meta_h=yes
ac_cv_header_minmax_h=yes
ac_cv_header_pvfs_config_h=yes
ac_cv_header_pvfs_h=yes
ac_cv_header_pvfs_proto_h=yes
ac_cv_header_pvfs_types_h=yes
ac_cv_header_req_h=yes
ac_cv_header_stdc=yes
ac_cv_header_stdint_h=yes
ac_cv_header_stdlib_h=yes
ac_cv_header_string_h=yes
ac_cv_header_strings_h=yes
ac_cv_header_sys_ioctl_h=yes
ac_cv_header_sys_stat_h=yes
ac_cv_header_sys_time_h=yes
ac_cv_header_sys_types_h=yes
ac_cv_header_time=yes
ac_cv_header_unistd_h=yes
ac_cv_host=i686-pc-linux-gnu
ac_cv_host_alias=i686-pc-linux-gnu
ac_cv_lib_minipvfs_connect_timeout=yes
ac_cv_lib_minipvfs_pvfs_open=yes
ac_cv_objext=o
ac_cv_path_install='/usr/bin/install -c'
ac_cv_prog_CPP='gcc -E'
ac_cv_prog_HAVE_CUT=yes
ac_cv_prog_HAVE_GREP=yes
ac_cv_prog_HAVE_UNAME=yes
ac_cv_prog_ac_ct_CC=gcc
ac_cv_prog_cc_g=yes
ac_cv_prog_cc_stdc=
ac_cv_prog_gcc_traditional=no
ac_cv_type_signal=void
ac_cv_type_size_t=yes
## ------------ ##
## confdefs.h. ##
## ------------ ##
#define STDC_HEADERS 1
#define HAVE_SYS_TYPES_H 1
#define HAVE_SYS_STAT_H 1
#define HAVE_STDLIB_H 1
#define HAVE_STRING_H 1
#define HAVE_MEMORY_H 1
#define HAVE_STRINGS_H 1
#define HAVE_INTTYPES_H 1
#define HAVE_STDINT_H 1
#define HAVE_UNISTD_H 1
#define TIME_WITH_SYS_TIME 1
#define RETSIGTYPE void
#define HAVE_SELECT 1
#define HAVE_LIBMINIPVFS 1
#define HAVE_LIBMINIPVFS 1
#define STDC_HEADERS 1
#define HAVE_FCNTL_H 1
#define HAVE_MALLOC_H 1
#define HAVE_SYS_IOCTL_H 1
#define HAVE_SYS_TIME_H 1
#define HAVE_UNISTD_H 1
#define HAVE_LINUX_POSIX_TYPES_H 1
#define HAVE_LINUX_SLAB_H 1
#define HAVE_LINUX_TQUEUE_H 1
#define HAVE_LINUX_VMALLOC_H 1
#define HAVE_LINUX_PAGEMAP_H 1
#define HAVE_LINUX_LOCKS_H 1
#define HAVE_LINUX_SMP_LOCK_H 1
#define HAVE_LINUX_HIGHMEM_H 1
#define HAVE_LINUX_MODVERSIONS_H 1
#define HAVE_LINUX_MALLOC_H 1
#define HAVE_LINUX_INIT_H 1
#define HAVE_LINUX_SEQ_FILE_H 1
#define HAVE_SMP_KERNEL 1
#define HAVE_MODVERSIONS 1
#define HAVE_HIGHMEM 1
#define HAVE_LINUX_STRUCT_SUPER_BLOCK_S_MAXBYTES 1
#define HAVE_DEPRECATED_LINUX_MALLOC_H 1
configure: exit 0
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