I have Ubuntu 14.04 , I've installed JULIA, and then I tried to install IJULIA, writting Pkg.add("IJulia") on julia, but this appears:
signal (4): Illegal instruction
_mapreduce at ./reduce.jl:168
prune_versions at ./pkg/query.jl:141
prune_dependencies at ./pkg/query.jl:335
jl_trampoline at /usr/bin/../lib/i386-linux-gnu/julia/libjulia.so (unknown line)
jl_apply_generic at /usr/bin/../lib/i386-linux-gnu/julia/libjulia.so (unknown line)
resolve at ./pkg/entry.jl:379
edit at pkg/entry.jl:24
jl_trampoline at /usr/bin/../lib/i386-linux-gnu/julia/libjulia.so (unknown line)
jl_apply_generic at /usr/bin/../lib/i386-linux-gnu/julia/libjulia.so (unknown line)
anonymous at task.jl:340
jl_trampoline at /usr/bin/../lib/i386-linux-gnu/julia/libjulia.so (unknown line)
unknown function (ip: -1230846045)
unknown function (ip: -1230845923)
julia_trampoline at /usr/bin/../lib/i386-linux-gnu/julia/libjulia.so (unknown line)
unknown function (ip: 134516370)
__libc_start_main at /lib/i386-linux-gnu/libc.so.6 (unknown line)
unknown function (ip: 134516419)
Illegal instruction (core dumped)
Do any one knows what to do? What I want to achieve is to run ipython notebook --profile julia
Related
I have compiled this code:
program mpisimple
implicit none
integer ierr
include 'mpif.h'
call mpi_init(ierr)
write(6,*) 'Hello World!'
call mpi_finalize(ierr)
end
using the command: mpif90 -o helloworld simplempi.f90
When I run with this command:
$ mpiexec -np 1 ./helloworld
Hello World!
it works fine as you can see. But when I run with any other number of processors (here 4) I get the errors and I basically have to ctrl+C to kill it.
Fatal error in MPI_Init: Other MPI error, error stack:
MPIR_Init_thread(805).....: fail failed
MPID_Init(1859)...........: channel initialization failed
MPIDI_CH3_Init(126).......: fail failed
MPID_nem_init_ckpt(858)...: fail failed
MPIDI_CH3I_Seg_commit(427): PMI_KVS_Get returned 4
In: PMI_Abort(69777679, Fatal error in MPI_Init: Other MPI error, error stack:
MPIR_Init_thread(805).....: fail failed
MPID_Init(1859)...........: channel initialization failed
MPIDI_CH3_Init(126).......: fail failed
MPID_nem_init_ckpt(858)...: fail failed
MPIDI_CH3I_Seg_commit(427): PMI_KVS_Get returned 4)
forrtl: severe (174): SIGSEGV, segmentation fault occurred
What could be the problem? I am doing this on a Linux hpc system.
I figured out why this happened. The system I am using does not require users to submit single-core jobs through the scheduler, but does require it for multi-core jobs. Once the mpiexec command was submitted through a PBS bash script, the errors went away and output was as expected.
EDIT I had a typo in my command to launch lldb (see comment below) and I'm updating the post to get to a different larger issue
I'm trying to debug my MPI application in lldb and upon an error (e.g., segv or abort). Here's how I'm invoking my mpi run:
/usr/local/bin/mpiexec -np 3 -disable-auto-cleanup xterm -e "lldb -s lldb.commands -- app_binary <args> ; sleep 100
Immediately when I start running, I get this error trace. I think the most relevant line is PMI_Get_appnum returned -1
[cli_0]: write_line error; fd=8 buf=:cmd=init pmi_version=1 pmi_subversion=1
:
system msg for write_line failure : Bad file descriptor
[cli_0]: Unable to write to PMI_fd
[cli_0]: write_line error; fd=8 buf=:cmd=get_appnum
:
system msg for write_line failure : Bad file descriptor
Fatal error in MPI_Init_thread: Other MPI error, error stack:
MPIR_Init_thread(565):
MPID_Init(175).......: channel initialization failed
MPID_Init(463).......: PMI_Get_appnum returned -1
[cli_0]: write_line error; fd=8 buf=:cmd=abort exitcode=1094415
:
system msg for write_line failure : Bad file descriptor
Process 19063 exited with status = 15 (0x0000000f)
Unfortunately, some mailing lists show that this is a general bug with MPICH on OSX (see https://github.com/pmodels/mpich/issues/2063 -- currently still unresolved). Does anyone have a workaround?
Since you're using lldb and you're probably also using clang, you could use something called the address sanitizer to compile your code with runtime checks for memory errors.
Just add the following to your compile command: -g -fsanitize=address -fno-omit-frame-pointer -fsanitize-recover=address. It would look like
mpicc object.o -o exec -g -fsanitize=address -fno-omit-frame-pointer -fsanitize-recover=address
When using the address sanitizer your code will print a small stack trace to when you made a move to index out of bounds or address memory you don't own.
If you combine the address sanitizer with lldb then it should stop the execution at the line where a memory problem occurred. Although, I haven't had much success with running lldb and MPI at the same time. Either way the address sanitizer should help you.
conman version:
conman.x86_64 0.2.5-2.4.el6 #rhel-install
conman.conf
server syslog="local4"
global ipmiopts="admin,Password#_"
global log="/home/tops/%N.log"
global logopts="nosanitize,timestamp"
console name="17B001682" dev="ipmi:10.153.107.105"
running output:
[tops#HP380 ~]$ sudo /etc/init.d/conman restart
Starting ConMan: ERROR: CONFIG[/home/tops/conman.conf:2]: unrecognized token 'ipmiopts'
ERROR: CONFIG[/home/tops/conman.conf:6]: console [17B001682] device "ipmi:10.153.107.105" type unrecognized
ERROR: Configuration "/home/tops/conman.conf" has no consoles defined
[FAILED]
Why this error takes place and how can I fix it? thanks!
I have a simple Vagrantfile:
Vagrant.configure(2) do |config|
config.omnibus.chef_version = '12.9.38'
config.vm.network "private_network", type: "dhcp"
config.vm.boot_timeout = 60
config.vm.define "node0" do |node0|
node0.vm.box = "baremettle/ubuntu-14.04"
node0.vm.hostname = "node0"
node0.vm.synced_folder "./", "/vagrant", type: "rsync"
node0.vm.provider :libvirt do |qemu|
qemu.driver = "kvm"
qemu.memory = 1024
end
end
end
And when I try to bring machine up I get the following:
The following SSH command responded with a non-zero exit status.
Vagrant assumes that this means the command failed!
sh install.sh -v 12.9.38 2>&1
Stdout from the command:
ubuntu 14.04 x86_64
Getting information for chef stable 12.9.38 for ubuntu...
downloading https://omnitruck-direct.chef.io/stable/chef/metadata?v=12.9.38&p=ubuntu&pv=14.04&m=x86_64
to file /tmp/install.sh.1550/metadata.txt
trying wget...
trying perl...
trying python...
Unable to retrieve a valid package!
Version: 12.9.38
Please file a Bug Report at https://github.com/chef/omnitruck/issues/new
Alternatively, feel free to open a Support Ticket at https://www.chef.io/support/tickets
More Chef support resources can be found at https://www.chef.io/support
Please include as many details about the problem as possible i.e., how to reproduce
the problem (if possible), type of the Operating System and its version, etc.,
and any other relevant details that might help us with troubleshooting.
Metadata URL: https://omnitruck-direct.chef.io/stable/chef/metadata?v=12.9.38&p=ubuntu&pv=14.04&m=x86_64
DEBUG OUTPUT FOLLOWS:
STDERR from wget:
--2016-06-13 15:54:03-- https://omnitruck-direct.chef.io/stable/chef/metadata?v=12.9.38&p=ubuntu&pv=14.04&m=x86_64
Resolving omnitruck-direct.chef.io (omnitruck-direct.chef.io)... failed: Name or service not known.
wget: unable to resolve host address ‘omnitruck-direct.chef.io’
STDERR from perl:
Can't locate LWP/Simple.pm in #INC (you may need to install the LWP::Simple module) (#INC contains: /etc/perl /usr/local/lib/perl/5.18.2 /usr/local/share/perl/5.18.2 /usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.18 /usr/share/perl/5.18 /usr/local/lib/site_perl .) at -e line 1.
BEGIN failed--compilation aborted at -e line 1.
STDERR from python:
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/usr/lib/python2.7/urllib2.py", line 127, in urlopen
return _opener.open(url, data, timeout)
File "/usr/lib/python2.7/urllib2.py", line 404, in open
response = self._open(req, data)
File "/usr/lib/python2.7/urllib2.py", line 422, in _open
'_open', req)
File "/usr/lib/python2.7/urllib2.py", line 382, in _call_chain
result = func(*args)
File "/usr/lib/python2.7/urllib2.py", line 1222, in https_open
return self.do_open(httplib.HTTPSConnection, req)
File "/usr/lib/python2.7/urllib2.py", line 1184, in do_open
raise URLError(err)
urllib2.URLError: <urlopen error [Errno -2] Name or service not known>
Stderr from the command:
And after that machine is runnign but chef is not installed. And is I ssh into it and try to ping, for example, google.com, I will get:
vagrant#node0:~$ ping google.com
ping: unknown host google.com
But on host machine ping works as expected, without problems.
I'm using default libvirt network:
<network>
<name>default</name>
<uuid>bd07c4da-891b-4e37-b1d0-16fabb6581c2</uuid>
<forward mode='nat'>
<nat>
<port start='1024' end='65535'/>
</nat>
</forward>
<bridge name='virbr0' stp='on' delay='0'/>
<mac address='52:54:00:79:b9:3b'/>
<ip address='192.168.122.1' netmask='255.255.255.0'>
<dhcp>
<range start='192.168.122.2' end='192.168.122.254'/>
</dhcp>
</ip>
</network>
Vagrant version is 1.8.1
Virsh version is 1.2.2
Vagrant plugins installed:
vagrant-libvirt (0.0.33)
vagrant-omnibus (1.4.1)
UPDATE:
Adding to hosts(or guests) /etc/resolv.conf
nameserver 8.8.8.8
seems to solve the issue.
But I've never had that problem with virtualbox. Could it be that I missed something in libvirt or vagrant configuration?
I have a Vagrant machine based on VirtualBox that has some problems (see Vagrant crashes depending on physical network). Now I tried running it on another piece of hardware (with OS X Mavericks), and got the following error message:
There was an error while executing `VBoxManage`, a CLI used by Vagrant
for controlling VirtualBox. The command and stderr is shown below.
Command: ["hostonlyif", "create"]
Stderr: VBoxManage: error: Unable to create a host network interface
VBoxManage: error: Details: code NS_ERROR_FAILURE (0x80004005), component Host,
interface IHost, callee nsISupports
Context: "CreateHostOnlyNetworkInterface (hif.asOutParam(),
progress.asOutParam())" at line 64 of file VBoxManageHostonly.cpp
What does this mean?
For the error to appear I run
$ vagrant up
Bringing machine 'default' up with 'virtualbox' provider...
[default] Clearing any previously set forwarded ports...
[default] Creating shared folders metadata...
[default] Clearing any previously set network interfaces...
… and then it crashes. Any ideas?
Oh, by the way: It's Vagrant 1.3.5 and VirtualBox 4.1.18.
sudo /Library/StartupItems/VirtualBox/VirtualBox restart
worked for me, see https://coderwall.com/p/ydma0q
The popular answer seems to be modprobe vboxnetadp (for Linux) or /Library/StartupItems/VirtualBox/VirtualBox restart (for Mac).
However, the fix for me was to add myself to the vboxusers group and relogin.