[mpich-discuss] Segmentation Fault when running any application.

Sun Nov 20 11:34:43 CST 2011

One more question concerning this whole setup. If I wanted to compile an
MPI program that used OpenMP, how would I go about doing that? I have tried
to compile it but just adding the -fopenmp flag but when I tried to run the
program using mpiexec the program did nothing. There was no compilation
error or anything. When I commented out the lines concerning OpenMP, the
program ran fine.

On Fri, Nov 18, 2011 at 3:23 PM, Jayesh Krishna <jayesh at mcs.anl.gov> wrote:

>  Glad to know it worked for you.
>  The error messages are still annoying though. There are some known bugs
> with SMPD that might give these error messages (as you have already found)
> but unfortunately I haven't been able to recreate it here (Also we don't
> have dev resources to pursue this SMPD bug. So unfortunately you are stuck
> with the bug if you use SMPD.).
>
> Regards,
> Jayesh
>
> ----- Original Message -----
> From: "Michael Warthon" <michael.warthon at upr.edu>
> To: "Jayesh Krishna" <jayesh at mcs.anl.gov>
> Cc: mpich-discuss at mcs.anl.gov
>  Sent: Friday, November 18, 2011 2:36:59 PM
> Subject: Re: [mpich-discuss] Segmentation Fault when running any
> application.
>
> Oh my god! It finally worked! Yes, apparently it was that I was compiling
> it for the 64-bit version of MPICH2. I ran the code and it worked fine even
> though it was giving me the error concerning the left socket in mpiexec.
> Since it is working correctly, I think everything is okay now. Thank you
> very much for helping me out these past couple of days. I greatly
> appreciate it!
>
>
> On Fri, Nov 18, 2011 at 2:11 PM, Jayesh Krishna < jayesh at mcs.anl.gov >
> wrote:
>
>
> Hi,
> Do you have a 64-bit version of MPICH2 installed in your system ? If so,
> you need to create 64-bit executable with gcc (Use "-m64" flag of gcc OR
> use mingw compilers that accept "-m64" option) .
>
> (PS: On 64-bit systems I use mingw compilers,
> x86_64-w64-mingw32-g++ -I"/cygdrive/c/Program Files/MPICH2/include"
> -L"/cygdrive/c/Program Files/MPICH2/lib" hellow.c -lmpi
>
> )
>
> Regards,
> Jayesh
>
> ----- Original Message -----
> From: "Michael Warthon" < michael.warthon at upr.edu >
> To: "Jayesh Krishna" < jayesh at mcs.anl.gov >
> Cc: mpich-discuss at mcs.anl.gov
>
>
>
> Sent: Friday, November 18, 2011 12:04:05 PM
> Subject: Re: [mpich-discuss] Segmentation Fault when running any
> application.
>
>
> Alright I entered that command in and the result was this:
>
> /tmp/cc0GoDvV.o:hello.c:(.text+0x1f): undefined reference to `_MPI_Init'
> /tmp/cc0GoDvV.o:hello.c:(.text+0x36): undefined reference to
> `_MPI_Comm_size'
> /tmp/cc0GoDvV.o:hello.c:(.text+0x4d): undefined reference to
> `_MPI_Comm_rank'
> /tmp/cc0GoDvV.o:hello.c:(.text+0x64): undefined reference to
> `_MPI_Get_processor
> _name'
> /tmp/cc0GoDvV.o:hello.c:(.text+0x93): undefined reference to
> `_MPI_Finalize'
> collect2: ld returned 1 exit status
>
>
> On Fri, Nov 18, 2011 at 11:52 AM, Jayesh Krishna < jayesh at mcs.anl.gov >
> wrote:
>
>
> Hi,
> Try,
>
> $ gcc -I "/cygdrive/c/Program Files/MPICH2/include" -L
> "/cygdrive/c/Program Files/MPICH2/lib" hello.c -o hello.exe -lmpi
>
>
> Regards,
> Jayesh
>
> ----- Original Message -----
> From: "Michael Warthon" < michael.warthon at upr.edu >
> To: "Jayesh Krishna" < jayesh at mcs.anl.gov >
> Cc: mpich-discuss at mcs.anl.gov
>
>
>
> Sent: Friday, November 18, 2011 11:19:11 AM
> Subject: Re: [mpich-discuss] Segmentation Fault when running any
> application.
>
>
> If the program I am trying to compile will work with mpiexec even with the
> error present, then I will not install MPICH2 from source. Currently the
> command I am entering is:
>
> $ gcc hello.c -o hello.exe -I "/cygdrive/c/Program Files/MPICH2/include"
> -L "/cygdrive/c/Program Files/MPICH2/lib/libmpi.a" -lmpi
>
> The response I get is:
>
> /usr/lib/gcc/i686-pc-cygwin/4.5.3/../../../../i686-pc-cygwin/bin/ld:
> cannot find
> -lmpi
> collect2: ld returned 1 exit status
>
> Is there a verbose option for gcc in order to obtain more information
> about what is happening?
>
> On Fri, Nov 18, 2011 at 10:32 AM, Jayesh Krishna < jayesh at mcs.anl.gov >
> wrote:
>
>
> Hi,
> If you are not too much concerned about performance you can
> configure/make/install MPICH2 from source on Cygwin.
> If you want help with compiling an MPI program with gcc libs please send
> us the complete command that you used to compile your code (From the error
> message it looks like you did not specify the path to libmpi.a , you need
> to specify the path using "-L" option).
>
> (PS: Please provide as much details as possible)
>
> Regards,
> Jayesh
>
> ----- Original Message -----
> From: "Michael Warthon" < michael.warthon at upr.edu >
>
> To: "Jose Marques" < jmarques at itn.pt >, "Jayesh Krishna" <
> jayesh at mcs.anl.gov >
> Cc: mpich-discuss at mcs.anl.gov
>
>
>
> Sent: Thursday, November 17, 2011 2:54:37 PM
> Subject: Re: [mpich-discuss] Segmentation Fault when running any
> application.
>
>
> Ok well I did a bit of searching on past discussions and it looks like the
> error will come up but won't affect how the program will run. However, it
> seems that I keep getting out of one problem and running into another. When
> I tried to compile the hello.c file again I got this error:
>
> /usr/lib/gcc/i686-pc-cygwin/4.5.3/../../../../i686-pc-cygwin/bin/ld:
> cannot find
> -lmpi
> collect2: ld returned 1 exit status
>
> I want to make sure that other executable will work for mpiexec so I would
> like to be able to compile hello.c and then test to see if it will run or
> not.
>
>
> On Thu, Nov 17, 2011 at 12:38 PM, Michael Warthon <
> michael.warthon at upr.edu > wrote:
>
>
> Thank you. Unfortunately I still get the same error regarding the closing
> of the left context socket.
>
>
>
>
>
> On Thu, Nov 17, 2011 at 2:28 PM, Jose Marques < jmarques at itn.pt > wrote:
>
>
>
> Michael,
>
> There's a good set of instructions in
> http://www.petri.co.il/disable-uac-in-windows-7.htm
>
> Rds,
> Jose
>
>
>
>
> On 17-11-2011 6:12, Michael Warthon wrote:
>
>
>
> How do I go about turning that off?
>
>
>
> On Nov 17, 2011, at 2:05 PM, Jose Marques < jmarques at itn.pt > wrote:
>
>
>
>
> Michael,
>
> Did you switch off User Account Control in Windows 7 ? I think I had the
> same probs and solved them taking care of UAC.
>
> Jose
>
> On 17-11-2011 5:35, Michael Warthon wrote:
>
> I am still getting the same error even after reinstalling SMPD. The MPICH2
> that I have installed is the 64-bit version. My computer has windows 7, is
> a 64-bit operating system, and has an intel core i5 CPU processor. The
> installer I used mpich2-1.4.1p1-win-x86-64.msi is the correct one right?
>
>
> On Thu, Nov 17, 2011 at 12:22 PM, Jayesh Krishna < jayesh at mcs.anl.gov >
> wrote:
>
>
> Hi,
> The error message does not appear with the "-verbose" option (The launch
> mechanism with a "-verbose" option is different though).
> I think that the issue is still that MPICH2 was not installed correctly in
> your system (I verified that 1.4.1p1 works correctly - without error msgs -
> on our Srv2008). Please follow the steps below and let us know if it works
> for you,
>
> # Right-click on the command prompt icon and select "Run as administrator"
> to open an admin command prompt
> # From the admin command prompt, uninstall SMPD using the "-uninstall"
> option (Type "smpd -uninstall")
> # From the admin command prompt, install SMPD using the "-install" option
> (Type "smpd -install")
> # Try running mpiexec from the admin command prompt (Type "mpiexec -n 2
> hostname")
> # Try running mpiexec from a normal command prompt (Type "mpiexec -n 2
> hostname")
>
> Let us know the results.
>
>
> Regards,
> Jayesh
>
> ----- Original Message -----
> From: "Michael Warthon" < michael.warthon at upr.edu >
> To: "Jayesh Krishna" < jayesh at mcs.anl.gov >
> Cc: mpich-discuss at mcs.anl.gov
>
>
> Sent: Thursday, November 17, 2011 10:10:28 AM
> Subject: Re: [mpich-discuss] Segmentation Fault when running any
> application.
>
>
> Alright. Attached is the text file with the complete message from the
> command: "c:\Program Files\MPICH2\bin\mpiexec" -verbose -n 2 hostname
>
> I tried the other command and for some reason I am actually able to run
> the program even when the errors occur. This is the response I got when
> running the command:
>
> C:\Users\Mike>"c:\Program Files\MPICH2\bin\mpiexec" -n 2 "C:\Program
> Files\MPICH
> 2\examples\cpi.exe"
> error closing the left context socket: Error = -1
> Enter the number of intervals: (0 quits) 100
> pi is approximately 3.1416009869231241, Error is 0.0000083333333309
> wall clock time = 0.000541
> Enter the number of intervals: (0 quits) 10
> pi is approximately 3.1424259850010983, Error is 0.0008333314113051
> wall clock time = 0.000047
> Enter the number of intervals: (0 quits) 0
> op_read error on left context: Error = -1
> unable to read the cmd header on the left context, Error = -1
> .
> Error posting readv, An existing connection was forcibly closed by the
> remote ho
> st.(10054)
>
>
> On Thu, Nov 17, 2011 at 9:56 AM, Jayesh Krishna < jayesh at mcs.anl.gov >
> wrote:
>
>
> Hi,
> Yes, please give us the output of the command with "-verbose" turned on.
> And for these tests, run mpiexec with the complete path ("c:\Program
> Files\MPICH2\bin\mpiexec" -verbose -n 2 hostname). Do you get the same
> error message when executing cpi ("c:\Program Files\MPICH2\bin\mpiexec" -n
> 2 "C:\Program Files\MPICH2\examples\cpi.exe")?
>
>
> Regards,
> Jayesh
>
> ----- Original Message -----
> From: "Michael Warthon" < michael.warthon at upr.edu >
> To: "Jayesh Krishna" < jayesh at mcs.anl.gov >
> Cc: mpich-discuss at mcs.anl.gov
>
>
>
> Sent: Thursday, November 17, 2011 9:42:42 AM
> Subject: Re: [mpich-discuss] Segmentation Fault when running any
> application.
>
>
> For each command, this is the entire response that I get:
>
>
> C:\Users\Mike>mpiexec -validate
> SUCCESS
>
> C:\Users\Mike>mpiexec -n 2 hostname
> error closing the left context socket: Error = -1
>
> Mike-PC
> Mike-PC
> error closing the left context socket: Error = -1
>
> C:\Users\Mike>
>
>
> Did you want me to use the verbose option?
>
> On Thu, Nov 17, 2011 at 9:21 AM, Jayesh Krishna < jayesh at mcs.anl.gov >
> wrote:
>
>
> Hi,
> Please copy-paste the command and the response (the complete message) in
> your email.
> Are you able to validate the registered username/password (Type "mpiexec
> -validate" and it should return "SUCCESS")?
>
>
> Regards,
> Jayesh
>
> ----- Original Message -----
> From: "Michael Warthon" < michael.warthon at upr.edu >
> To: "Jayesh Krishna" < jayesh at mcs.anl.gov >
>
>
>
> Cc: mpich-discuss at mcs.anl.gov
> Sent: Thursday, November 17, 2011 7:50:25 AM
> Subject: Re: [mpich-discuss] Segmentation Fault when running any
> application.
>
> Ok. I have checked and yes smpd is running and I have given a sufficient
> username and password so that mpiexec will run. Now I am getting a new
> error when executing mpiexec -n 2 hostname where it is giving me this
> response:
>
> error closing the left context socket: Error = -1
>
>
> On Wed, Nov 16, 2011 at 2:21 PM, Jayesh Krishna < jayesh at mcs.anl.gov >
> wrote:
>
>
> Hi,
>
> 1. Make sure that the process manager, smpd, is running in your system
> (Look in the task manager/Process Explorer to see if there is a service
> named smpd running. Alternately you can run "smpd -status" to check if smpd
> is running)
>
> 2. Run a simple non-MPI program like hostname from the command prompt
> using mpiexec (Type "mpiexec -n 2 hostname" ). When prompted for
> username/password give a valid Windows username/password.
> If mpiexec gives you an error, type "mpiexec -remove" to remove the
> existing registered username/password and then type "mpiexec -register" to
> register a new/valid Windows username/password. Re-run mpiexec.
>
> 3. Run the sample MPI program, cpi.exe, provided with MPICH2 (mpiexec -n 2
> C:\Progra~1\MPICH2\examples\cpi.exe)
>
> >> I am getting an error when I look at the MPICH2 configurable settings
> ...
>
> This is a known bug. Due to limited developer bandwidth we haven't been
> able to address this issue yet.
>
>
> Regards,
> Jayesh
>
> ----- Original Message -----
> From: "Michael Warthon" < michael.warthon at upr.edu >
> To: "Jayesh Krishna" < jayesh at mcs.anl.gov >
>
> Sent: Wednesday, November 16, 2011 12:27:01 PM
> Subject: Re: [mpich-discuss] Segmentation Fault when running any
> application.
>
>
>
> Alright. I have reinstalled MPICH2 using the method in section 9.4.
> However, I am not able to connect to the host it seems. I keep receiving
> this message when trying to execute a program:
>
>
>
> Credentials for Mike rejected connecting to Mike-PC
>
> Aborting: Unable to connect to Mike-PC
> Also, I am getting an error when I look at the MPICH2 configurable
> settings that says that MPICH2 is not installed or that it cannot query the
> host.
>
> On Wed, Nov 16, 2011 at 9:35 AM, Jayesh Krishna < jayesh at mcs.anl.gov >
> wrote:
>
>
> Hi,
> Looks like MPICH2 was not installed correctly in your system.
> Uninstall your existing version of MPICH2. Please follow the steps in
> Section 9.4 (Not 9.1 -
> http://www.mcs.anl.gov/research/projects/mpich2/documentation/files/mpich2-1.4.1-installguide.pdf) of the installer's guide to install MPICH2.
>
>
>
>
> (PS: I am assuming that you have Win7/Srv2008/...)
>
> Regards,
> Jayesh
>
> ----- Original Message -----
> From: "Michael Warthon" < michael.warthon at upr.edu >
> To: "Jayesh Krishna" < jayesh at mcs.anl.gov >
>
>
>
> Sent: Tuesday, November 15, 2011 9:04:57 PM
> Subject: Re: [mpich-discuss] Segmentation Fault when running any
> application.
>
>
> Yeah it must have been that I got the installation mixed up. I downloaded
> the windows installer and it finally compiled. So progess has been made as
> now I am getting this error when trying to run hello.exe:
>
>
>
> Error while connecting to host, No connection could be made because the
> target m
>
> achine actively refused it. (10061)
>
> Connect on sock (host=localhost, port=8676) failed, exhaused all end points
>
> Unable to connect to 'localhost:8676',
>
> sock error: Error = -1
>
>
> On Tue, Nov 15, 2011 at 5:12 PM, Jayesh Krishna < jayesh at mcs.anl.gov >
> wrote:
>
>
> Hi,
> There are two ways you can use MPICH2 on Windows+cygwin,
>
> # Download MPICH2 source compile/install it on Cygwin. Use mpicc to
> compile and use mpiexec (from this installation - NOT the one available
> with Windows installer) to run your program.
>
> # Download MPICH2 Windows installer, install MPICH2 (using installer gui).
> Use the cygwin/gcc libs provided with the Windows installation to compile
> your code. Use mpiexec from the Windows installation to run your job.
>
> Looks like you are mixing the approaches.
>
>
> Regards,
> Jayesh
>
> ----- Original Message -----
> From: "Michael Warthon" < michael.warthon at upr.edu >
> To: "Jayesh Krishna" < jayesh at mcs.anl.gov >
>
>
>
> Sent: Tuesday, November 15, 2011 1:03:02 PM
> Subject: Re: [mpich-discuss] Segmentation Fault when running any
> application.
>
>
> I was using mpicc in order to compile it. Unfortunately I am still not
> able to compile the code even with the command you gave me. I used:
>
> gcc -l/mpich_install/include -L/mpich_install/lib hello.c -lmpi
>
> I still received the same error. Did I install it incorrectly maybe?
>
> On Tue, Nov 15, 2011 at 12:42 PM, Jayesh Krishna < jayesh at mcs.anl.gov >
> wrote:
>
>
> Hi,
> How were you compiling your code before ?
> A command similar to,
>
> "gcc -I/cygdrive/c/Progra~1/MPICH2/include
> -L/cygdrive/c/Progra~1/MPICH2/lib hello.c -o hello.exe -lmpi"
>
> should work.
>
>
> Regards,
> jayesh
>
> ----- Original Message -----
> From: "Michael Warthon" < michael.warthon at upr.edu >
> To: "Jayesh Krishna" < jayesh at mcs.anl.gov >
>
>
>
> Sent: Tuesday, November 15, 2011 12:18:43 PM
> Subject: Re: [mpich-discuss] Segmentation Fault when running any
> application.
>
>
> Alright. Well I tried it and for some reason it is not able to see the
> library.
> I used the command:
> gcc -g hello.c -L\mpich_install\lib -lmpi
>
> It ended up giving me an error saying:
> fatal error: mpi.h: No such file or directory
>
> On Tue, Nov 15, 2011 at 10:32 AM, Jayesh Krishna < jayesh at mcs.anl.gov >
> wrote:
>
>
> Hi,
> Try using gcc (usual gcc stuff: specify include dirs using "-I", lib dirs
> using "-L") to compile your code and link it with "-lmpi" .
>
>
> Regards,
> Jayesh
>
> ----- Original Message -----
> From: "Michael Warthon" < michael.warthon at upr.edu >
> To: "Jayesh Krishna" < jayesh at mcs.anl.gov >
>
>
>
> Sent: Tuesday, November 15, 2011 10:16:00 AM
> Subject: Re: [mpich-discuss] Segmentation Fault when running any
> application.
>
>
> What would be the correct command to use in cygwin in order to compile the
> code? Just want to make sure that I actually compiled it correctly.
>
>
> On Tue, Nov 15, 2011 at 10:10 AM, Jayesh Krishna < jayesh at mcs.anl.gov >
> wrote:
>
>
> Hi,
> I just tried compiling your code with cygwin gcc (3.4.4) + MPICH2 1.4.1p1
> gcc libs and it worked for me (No seg fault, gives the expected output).
> Make sure that you are using the correct header files and libraries
> (MPICH2 libs and headers) when you compile your code.
>
> Regards,
>
> Jayesh
>
> ----- Original Message -----
> From: "Michael Warthon" < michael.warthon at upr.edu >
>
>
>
> To: "Jayesh Krishna" < jayesh at mcs.anl.gov >
> Sent: Tuesday, November 15, 2011 9:53:32 AM
> Subject: Re: [mpich-discuss] Segmentation Fault when running any
> application.
>
> Ah sorry. I forgot to include the p1 at the end of it. I am using mpich2
> 1.4.1p1
>
>
> On Tue, Nov 15, 2011 at 9:44 AM, Jayesh Krishna < jayesh at mcs.anl.gov >
> wrote:
>
>
> Did you try the latest stable release (1.4.1p1)?
>
> -Jayesh
>
>
> ----- Original Message -----
> From: "Michael Warthon" < michael.warthon at upr.edu >
> To: mpich-discuss at mcs.anl.gov
> Sent: Monday, November 14, 2011 7:54:43 PM
> Subject: [mpich-discuss] Segmentation Fault when running any application.
>
>
>
> Hello,
>
> I am new to MPI and I went and installed mpich2 1.4.1 onto a windows
> system that is being used through cygwin. I have compiled the code that
> simply prints the process and rank as shown below.
>
>
>
> #include <stdio.h>
> #include <mpi.h>
>
> int main( int argc, char *argv[]) {
>
> int numprocs, rank, namelen;
> char processor_name[MPI_MAX_PROCESSOR_NAME];
>
> MPI_Init(&argc, &argv);
> MPI_Comm_size(MPI_COMM_WORLD, &numprocs);
> MPI_Comm_rank(MPI_COMM_WORLD, &rank);
> MPI_Get_processor_name(processor_name, &namelen);
>
> printf( "Process %d on %s out of %d\n" , rank, processor_name, numprocs);
>
> MPI_Finalize();
> }
>
> Nothing too complicated. However, I still receive an error from the
> command line in cygwin that simply reads segmentation fault: (core dumped).
> The command I used was:
>
> mpiexec -n 1 a.exe
>
> No matter what executable I try to run, I still receive the same error.
> Any help regarding this would be greatly appreciated!
> _______________________________________________
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>
>
> _______________________________________________
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> --
> Dr. Jose G. Marques
> Reactor Manager
> Instituto Tecnologico e Nuclear phone: (+351) 219 946 115 Estrada
> Nacional 10 fax: (+351) 219 941 039 P-2686-953 Sacavem, Portugal
> --
> Dr. Jose G. Marques
> Reactor Manager
> Instituto Tecnologico e Nuclear phone: (+351) 219 946 115 Estrada
> Nacional 10 fax: (+351) 219 941 039 P-2686-953 Sacavem, Portugal
>
>
>
>
>
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