[OMPI users] can not compile Openmpi-3.0

Discussion:

abhisek Mondal

2018-04-03 04:06:48 UTC

Hi,

I need some help regarding compiling Openmpi-3.0. I have perfectly working
C compiler, however, during configuration I'm keep getting this error:

*============================================================================*
*== Configuring Open MPI*
*============================================================================*

**** Startup tests*
*checking build system type... x86_64-unknown-linux-gnu*
*checking host system type... x86_64-unknown-linux-gnu*
*checking target system type... x86_64-unknown-linux-gnu*
*checking for gcc... gcc*
*checking whether the C compiler works... yes*
*checking for C compiler default output file name... a.out*
*checking for suffix of executables... *
*checking whether we are cross compiling... configure: error: in
`/home/user/openmpi-2.0.4':*
*configure: error: cannot run C compiled programs.*
*If you meant to cross compile, use `--host'.*
*See `config.log' for more details*

I do not know waht is cross compiling but how can I avoid this error ?
Please help me out here.

Thanks
--
Abhisek Mondal

*Senior Research Fellow*

*Structural Biology and Bioinformatics Division*
*CSIR-Indian Institute of Chemical Biology*

*Kolkata 700032*

*INDIA*

Gilles Gouaillardet

2018-04-03 04:17:52 UTC

Permalink

Can you please compress and attach your config.log ?

You might also want to double check you can compile *and* run a simple C
hello world program

Cheers,

Gilles

Post by abhisek Mondal
Hi,
I need some help regarding compiling Openmpi-3.0. I have perfectly
working C compiler, however, during configuration I'm keep getting
/============================================================================/
/== Configuring Open MPI/
/============================================================================/
/
/
/*** Startup tests/
/checking build system type... x86_64-unknown-linux-gnu/
/checking host system type... x86_64-unknown-linux-gnu/
/checking target system type... x86_64-unknown-linux-gnu/
/checking for gcc... gcc/
/checking whether the C compiler works... yes/
/checking for C compiler default output file name... a.out/
/checking for suffix of executables... /
/*checking whether we are cross compiling... configure: error: in
`/home/user/openmpi-2.0.4':*/
/configure: error: cannot run C compiled programs./
/If you meant to cross compile, use `--host'./
/See `config.log' for more details/
I do not know waht is cross compiling but how can I avoid this error ?
Please help me out here.
Thanks
--
Abhisek Mondal
/Senior Research Fellow
/
/Structural Biology and Bioinformatics Division
/
/CSIR-Indian Institute of Chemical Biology/
/Kolkata 700032
/
/INDIA
/
_______________________________________________
users mailing list
https://lists.open-mpi.org/mailman/listinfo/users

abhisek Mondal

2018-04-03 04:22:21 UTC

Permalink

Hello,

I have uploaded the config.log here:
https://drive.google.com/drive/u/0/folders/0B6O-L5Y7BiGJfmQ4N2FpblBEcFNxaDZnaGpsUFFEUlotVWFjajR0UFFHNk5aYlhoSHVTWkU

Post by Gilles Gouaillardet
Can you please compress and attach your config.log ?
You might also want to double check you can compile *and* run a simple C
hello world program
Cheers,
Gilles

Post by abhisek Mondal
Hi,
I need some help regarding compiling Openmpi-3.0. I have perfectly
working C compiler, however, during configuration I'm keep getting this
/===========================================================
=================/
/== Configuring Open MPI/
/===========================================================
=================/
/
/
/*** Startup tests/
/checking build system type... x86_64-unknown-linux-gnu/
/checking host system type... x86_64-unknown-linux-gnu/
/checking target system type... x86_64-unknown-linux-gnu/
/checking for gcc... gcc/
/checking whether the C compiler works... yes/
/checking for C compiler default output file name... a.out/
/checking for suffix of executables... /
/*checking whether we are cross compiling... configure: error: in
`/home/user/openmpi-2.0.4':*/
/configure: error: cannot run C compiled programs./
/If you meant to cross compile, use `--host'./
/See `config.log' for more details/
I do not know waht is cross compiling but how can I avoid this error ?
Please help me out here.
Thanks
--
Abhisek Mondal
/Senior Research Fellow
/
/Structural Biology and Bioinformatics Division
/
/CSIR-Indian Institute of Chemical Biology/
/Kolkata 700032
/
/INDIA
/
_______________________________________________
users mailing list
https://lists.open-mpi.org/mailman/listinfo/users

_______________________________________________
users mailing list
https://lists.open-mpi.org/mailman/listinfo/users

--
Abhisek Mondal

*Senior Research Fellow*

*Structural Biology and Bioinformatics Division*
*CSIR-Indian Institute of Chemical Biology*

*Kolkata 700032*

*INDIA*

Gilles Gouaillardet

2018-04-03 04:38:13 UTC

Permalink

This is the relevant part related to this error

configure:6620: checking whether we are cross compiling
configure:6628: gcc -o conftest conftest.c >&5
conftest.c:10:19: fatal error: stdio.h: No such file or directory
#include <stdio.h>
^
compilation terminated.
configure:6632: $? = 1
configure:6639: ./conftest
../configure: line 6641: ./conftest: No such file or directory
configure:6643: $? = 127

at the very least, you need to install the glibc-headers package

Cheers,

Gilles

Post by abhisek Mondal
Hello,
https://drive.google.com/drive/u/0/folders/0B6O-L5Y7BiGJfmQ4N2FpblBEcFNxaDZnaGpsUFFEUlotVWFjajR0UFFHNk5aYlhoSHVTWkU
Can you please compress and attach your config.log ?
You might also want to double check you can compile *and* run a
simple C hello world program
Cheers,
Gilles
Hi,
I need some help regarding compiling Openmpi-3.0. I have
perfectly working C compiler, however, during configuration
/============================================================================/
/== Configuring Open MPI/
/============================================================================/
/
/
/*** Startup tests/
/checking build system type... x86_64-unknown-linux-gnu/
/checking host system type... x86_64-unknown-linux-gnu/
/checking target system type... x86_64-unknown-linux-gnu/
/checking for gcc... gcc/
/checking whether the C compiler works... yes/
/checking for C compiler default output file name... a.out/
/checking for suffix of executables... /
in `/home/user/openmpi-2.0.4':*/
/configure: error: cannot run C compiled programs./
/If you meant to cross compile, use `--host'./
/See `config.log' for more details/
I do not know waht is cross compiling but how can I avoid this error ?
Please help me out here.
Thanks
--
Abhisek Mondal
/Senior Research Fellow
/
/Structural Biology and Bioinformatics Division
/
/CSIR-Indian Institute of Chemical Biology/
/Kolkata 700032
/
/INDIA
/
_______________________________________________
users mailing list
https://lists.open-mpi.org/mailman/listinfo/users
<https://lists.open-mpi.org/mailman/listinfo/users>
_______________________________________________
users mailing list
https://lists.open-mpi.org/mailman/listinfo/users
<https://lists.open-mpi.org/mailman/listinfo/users>
--
Abhisek Mondal
/Senior Research Fellow
/
/Structural Biology and Bioinformatics Division
/
/CSIR-Indian Institute of Chemical Biology/
/Kolkata 700032
/
/INDIA
/
_______________________________________________
users mailing list
https://lists.open-mpi.org/mailman/listinfo/users

abhisek Mondal

2018-04-03 05:28:13 UTC

Permalink

Hello,

Installing glibc moved the installation little bit but again stuck at
sanity check.
Location of config.log:
https://drive.google.com/drive/u/0/folders/0B6O-L5Y7BiGJfmQ4N2FpblBEcFNxaDZnaGpsUFFEUlotVWFjajR0UFFHNk5aYlhoSHVTWkU

$ cpp --version
cpp (GCC) 4.8.5 20150623 (Red Hat 4.8.5-16)
Copyright (C) 2015 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

I have gcc and gcc-c++ installed.

Post by Gilles Gouaillardet
This is the relevant part related to this error
configure:6620: checking whether we are cross compiling
configure:6628: gcc -o conftest conftest.c >&5
conftest.c:10:19: fatal error: stdio.h: No such file or directory
#include <stdio.h>
^
compilation terminated.
configure:6632: $? = 1
configure:6639: ./conftest
../configure: line 6641: ./conftest: No such file or directory
configure:6643: $? = 127
at the very least, you need to install the glibc-headers package
Cheers,
Gilles

Post by abhisek Mondal
Hello,
I have uploaded the config.log here: https://drive.google.com/drive
/u/0/folders/0B6O-L5Y7BiGJfmQ4N2FpblBEcFNxaDZnaGpsUFFEUlotVW
FjajR0UFFHNk5aYlhoSHVTWkU
Can you please compress and attach your config.log ?
You might also want to double check you can compile *and* run a
simple C hello world program
Cheers,
Gilles
Hi,
I need some help regarding compiling Openmpi-3.0. I have
perfectly working C compiler, however, during configuration
/===========================================================
=================/
/== Configuring Open MPI/
/===========================================================
=================/
/
/
/*** Startup tests/
/checking build system type... x86_64-unknown-linux-gnu/
/checking host system type... x86_64-unknown-linux-gnu/
/checking target system type... x86_64-unknown-linux-gnu/
/checking for gcc... gcc/
/checking whether the C compiler works... yes/
/checking for C compiler default output file name... a.out/
/checking for suffix of executables... /
in `/home/user/openmpi-2.0.4':*/
/configure: error: cannot run C compiled programs./
/If you meant to cross compile, use `--host'./
/See `config.log' for more details/
I do not know waht is cross compiling but how can I avoid this error ?
Please help me out here.
Thanks
-- Abhisek Mondal
/Senior Research Fellow
/
/Structural Biology and Bioinformatics Division
/
/CSIR-Indian Institute of Chemical Biology/
/Kolkata 700032
/
/INDIA
/
_______________________________________________
users mailing list
https://lists.open-mpi.org/mailman/listinfo/users
<https://lists.open-mpi.org/mailman/listinfo/users>
_______________________________________________
users mailing list
https://lists.open-mpi.org/mailman/listinfo/users
<https://lists.open-mpi.org/mailman/listinfo/users>
--
Abhisek Mondal
/Senior Research Fellow
/
/Structural Biology and Bioinformatics Division
/
/CSIR-Indian Institute of Chemical Biology/
/Kolkata 700032
/
/INDIA
/
_______________________________________________
users mailing list
https://lists.open-mpi.org/mailman/listinfo/users

_______________________________________________
users mailing list
https://lists.open-mpi.org/mailman/listinfo/users

--
Abhisek Mondal

*Senior Research Fellow*

*Structural Biology and Bioinformatics Division*
*CSIR-Indian Institute of Chemical Biology*

*Kolkata 700032*

*INDIA*

Gilles Gouaillardet

2018-04-03 05:51:20 UTC

Permalink

It looks like kernel-headers is required too

Cheers,

Gilles

Post by abhisek Mondal
Hello,
Installing glibc moved the installation little bit but again stuck at
sanity check.
https://drive.google.com/drive/u/0/folders/0B6O-L5Y7BiGJfmQ4N2FpblBEcFNxaDZnaGpsUFFEUlotVWFjajR0UFFHNk5aYlhoSHVTWkU
$ cpp --version
cpp (GCC) 4.8.5 20150623 (Red Hat 4.8.5-16)
Copyright (C) 2015 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
I have gcc and gcc-c++ installed.
On Tue, Apr 3, 2018 at 10:08 AM, Gilles Gouaillardet
This is the relevant part related to this error
configure:6620: checking whether we are cross compiling
configure:6628: gcc -o conftest conftest.c >&5
conftest.c:10:19: fatal error: stdio.h: No such file or directory
#include <stdio.h>
^
compilation terminated.
configure:6632: $? = 1
configure:6639: ./conftest
../configure: line 6641: ./conftest: No such file or directory
configure:6643: $? = 127
at the very least, you need to install the glibc-headers package
Cheers,
Gilles
Hello,
https://drive.google.com/drive/u/0/folders/0B6O-L5Y7BiGJfmQ4N2FpblBEcFNxaDZnaGpsUFFEUlotVWFjajR0UFFHNk5aYlhoSHVTWkU
<https://drive.google.com/drive/u/0/folders/0B6O-L5Y7BiGJfmQ4N2FpblBEcFNxaDZnaGpsUFFEUlotVWFjajR0UFFHNk5aYlhoSHVTWkU>
On Tue, Apr 3, 2018 at 9:47 AM, Gilles Gouaillardet
Can you please compress and attach your config.log ?
You might also want to double check you can compile *and*
run a
simple C hello world program
Cheers,
Gilles
Hi,
I need some help regarding compiling Openmpi-3.0. I have
perfectly working C compiler, however, during
configuration

/============================================================================/
/== Configuring Open MPI/

/============================================================================/
/
/
/*** Startup tests/
/checking build system type... x86_64-unknown-linux-gnu/
/checking host system type... x86_64-unknown-linux-gnu/
/checking target system type... x86_64-unknown-linux-gnu/
/checking for gcc... gcc/
/checking whether the C compiler works... yes/
/checking for C compiler default output file name...
a.out/
/checking for suffix of executables... /
/*checking whether we are cross compiling...
in `/home/user/openmpi-2.0.4':*/
/configure: error: cannot run C compiled programs./
/If you meant to cross compile, use `--host'./
/See `config.log' for more details/
I do not know waht is cross compiling but how can I
avoid this
error ?
Please help me out here.
Thanks
-- Abhisek Mondal
/Senior Research Fellow
/
/Structural Biology and Bioinformatics Division
/
/CSIR-Indian Institute of Chemical Biology/
/Kolkata 700032
/
/INDIA
/
_______________________________________________
users mailing list
https://lists.open-mpi.org/mailman/listinfo/users
<https://lists.open-mpi.org/mailman/listinfo/users>
<https://lists.open-mpi.org/mailman/listinfo/users
<https://lists.open-mpi.org/mailman/listinfo/users>>
_______________________________________________
users mailing list
https://lists.open-mpi.org/mailman/listinfo/users
<https://lists.open-mpi.org/mailman/listinfo/users>
<https://lists.open-mpi.org/mailman/listinfo/users
<https://lists.open-mpi.org/mailman/listinfo/users>>
--
Abhisek Mondal
/Senior Research Fellow
/
/Structural Biology and Bioinformatics Division
/
/CSIR-Indian Institute of Chemical Biology/
/Kolkata 700032
/
/INDIA
/
_______________________________________________
users mailing list
https://lists.open-mpi.org/mailman/listinfo/users
<https://lists.open-mpi.org/mailman/listinfo/users>
_______________________________________________
users mailing list
https://lists.open-mpi.org/mailman/listinfo/users
<https://lists.open-mpi.org/mailman/listinfo/users>
--
Abhisek Mondal
/Senior Research Fellow
/
/Structural Biology and Bioinformatics Division
/
/CSIR-Indian Institute of Chemical Biology/
/Kolkata 700032
/
/INDIA
/
_______________________________________________
users mailing list
https://lists.open-mpi.org/mailman/listinfo/users

abhisek Mondal

2018-04-03 06:51:44 UTC

Permalink

Thanks a lot. Installing the headers worked like a charm !

I have a question though. Why does configuration says:

Version: 3.0.1
Build MPI C bindings: yes
Build MPI C++ bindings (deprecated): no
Build MPI Fortran bindings: mpif.h, use mpi
MPI Build Java bindings (experimental): no
Build Open SHMEM support: yes
Debug build: no
Platform file: (none)

Miscellaneous
-----------------------
*CUDA support: no*

I have a single GPU on my machine. Do I need to define it manually while
configuring openmpi?

Post by Gilles Gouaillardet
It looks like kernel-headers is required too
Cheers,
Gilles

Post by abhisek Mondal
Hello,
Installing glibc moved the installation little bit but again stuck at
sanity check.
Location of config.log: https://drive.google.com/drive
/u/0/folders/0B6O-L5Y7BiGJfmQ4N2FpblBEcFNxaDZnaGpsUFFEUlotVW
FjajR0UFFHNk5aYlhoSHVTWkU
$ cpp --version
cpp (GCC) 4.8.5 20150623 (Red Hat 4.8.5-16)
Copyright (C) 2015 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
I have gcc and gcc-c++ installed.
This is the relevant part related to this error
configure:6620: checking whether we are cross compiling
configure:6628: gcc -o conftest conftest.c >&5
conftest.c:10:19: fatal error: stdio.h: No such file or directory
#include <stdio.h>
^
compilation terminated.
configure:6632: $? = 1
configure:6639: ./conftest
../configure: line 6641: ./conftest: No such file or directory
configure:6643: $? = 127
at the very least, you need to install the glibc-headers package
Cheers,
Gilles
Hello,
https://drive.google.com/drive/u/0/folders/0B6O-L5Y7BiGJfmQ4
N2FpblBEcFNxaDZnaGpsUFFEUlotVWFjajR0UFFHNk5aYlhoSHVTWkU
<https://drive.google.com/drive/u/0/folders/0B6O-L5Y7BiGJfmQ
4N2FpblBEcFNxaDZnaGpsUFFEUlotVWFjajR0UFFHNk5aYlhoSHVTWkU>
On Tue, Apr 3, 2018 at 9:47 AM, Gilles Gouaillardet
Can you please compress and attach your config.log ?
You might also want to double check you can compile *and* run a
simple C hello world program
Cheers,
Gilles
Hi,
I need some help regarding compiling Openmpi-3.0. I have
perfectly working C compiler, however, during
configuration
/===========================================================
=================/
/== Configuring Open MPI/
/===========================================================
=================/
/
/
/*** Startup tests/
/checking build system type... x86_64-unknown-linux-gnu/
/checking host system type... x86_64-unknown-linux-gnu/
/checking target system type... x86_64-unknown-linux-gnu/
/checking for gcc... gcc/
/checking whether the C compiler works... yes/
/checking for C compiler default output file name... a.out/
/checking for suffix of executables... /
/*checking whether we are cross compiling...
in `/home/user/openmpi-2.0.4':*/
/configure: error: cannot run C compiled programs./
/If you meant to cross compile, use `--host'./
/See `config.log' for more details/
I do not know waht is cross compiling but how can I
avoid this
error ?
Please help me out here.
Thanks
-- Abhisek Mondal
/Senior Research Fellow
/
/Structural Biology and Bioinformatics Division
/
/CSIR-Indian Institute of Chemical Biology/
/Kolkata 700032
/
/INDIA
/
_______________________________________________
users mailing list
https://lists.open-mpi.org/mailman/listinfo/users
<https://lists.open-mpi.org/mailman/listinfo/users>
<https://lists.open-mpi.org/mailman/listinfo/users
<https://lists.open-mpi.org/mailman/listinfo/users>>
_______________________________________________
users mailing list
https://lists.open-mpi.org/mailman/listinfo/users
<https://lists.open-mpi.org/mailman/listinfo/users>
<https://lists.open-mpi.org/mailman/listinfo/users
<https://lists.open-mpi.org/mailman/listinfo/users>>
-- Abhisek Mondal
/Senior Research Fellow
/
/Structural Biology and Bioinformatics Division
/
/CSIR-Indian Institute of Chemical Biology/
/Kolkata 700032
/
/INDIA
/
_______________________________________________
users mailing list
https://lists.open-mpi.org/mailman/listinfo/users
<https://lists.open-mpi.org/mailman/listinfo/users>
_______________________________________________
users mailing list
https://lists.open-mpi.org/mailman/listinfo/users
<https://lists.open-mpi.org/mailman/listinfo/users>
--
Abhisek Mondal
/Senior Research Fellow
/
/Structural Biology and Bioinformatics Division
/
/CSIR-Indian Institute of Chemical Biology/
/Kolkata 700032
/
/INDIA
/
_______________________________________________
users mailing list
https://lists.open-mpi.org/mailman/listinfo/users

_______________________________________________
users mailing list
https://lists.open-mpi.org/mailman/listinfo/users

--
Abhisek Mondal

*Senior Research Fellow*

*Structural Biology and Bioinformatics Division*
*CSIR-Indian Institute of Chemical Biology*

*Kolkata 700032*

*INDIA*

Gilles Gouaillardet

2018-04-03 07:07:02 UTC

Permalink

Did you install CUDA and where ?

Post by abhisek Mondal
Thanks a lot. Installing the headers worked like a charm !
Version: 3.0.1
Build MPI C bindings: yes
Build MPI C++ bindings (deprecated): no
Build MPI Fortran bindings: mpif.h, use mpi
MPI Build Java bindings (experimental): no
Build Open SHMEM support: yes
Debug build: no
Platform file: (none)
Miscellaneous
-----------------------
*CUDA support: no*
*
*
*
*
I have a single GPU on my machine. Do I need to define it manually
while configuring openmpi?
On Tue, Apr 3, 2018 at 11:21 AM, Gilles Gouaillardet
It looks like kernel-headers is required too
Cheers,
Gilles
Hello,
Installing glibc moved the installation little bit but again
stuck at sanity check.
https://drive.google.com/drive/u/0/folders/0B6O-L5Y7BiGJfmQ4N2FpblBEcFNxaDZnaGpsUFFEUlotVWFjajR0UFFHNk5aYlhoSHVTWkU
<https://drive.google.com/drive/u/0/folders/0B6O-L5Y7BiGJfmQ4N2FpblBEcFNxaDZnaGpsUFFEUlotVWFjajR0UFFHNk5aYlhoSHVTWkU>
$ cpp --version
cpp (GCC) 4.8.5 20150623 (Red Hat 4.8.5-16)
Copyright (C) 2015 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
I have gcc and gcc-c++ installed.
On Tue, Apr 3, 2018 at 10:08 AM, Gilles Gouaillardet
This is the relevant part related to this error
configure:6620: checking whether we are cross compiling
configure:6628: gcc -o conftest conftest.c >&5
conftest.c:10:19: fatal error: stdio.h: No such file or
directory
#include <stdio.h>
^
compilation terminated.
configure:6632: $? = 1
configure:6639: ./conftest
../configure: line 6641: ./conftest: No such file or directory
configure:6643: $? = 127
at the very least, you need to install the glibc-headers
package
Cheers,
Gilles
Hello,
https://drive.google.com/drive/u/0/folders/0B6O-L5Y7BiGJfmQ4N2FpblBEcFNxaDZnaGpsUFFEUlotVWFjajR0UFFHNk5aYlhoSHVTWkU
<https://drive.google.com/drive/u/0/folders/0B6O-L5Y7BiGJfmQ4N2FpblBEcFNxaDZnaGpsUFFEUlotVWFjajR0UFFHNk5aYlhoSHVTWkU>

<https://drive.google.com/drive/u/0/folders/0B6O-L5Y7BiGJfmQ4N2FpblBEcFNxaDZnaGpsUFFEUlotVWFjajR0UFFHNk5aYlhoSHVTWkU
<https://drive.google.com/drive/u/0/folders/0B6O-L5Y7BiGJfmQ4N2FpblBEcFNxaDZnaGpsUFFEUlotVWFjajR0UFFHNk5aYlhoSHVTWkU>>
On Tue, Apr 3, 2018 at 9:47 AM, Gilles Gouaillardet
Can you please compress and attach your config.log ?
You might also want to double check you can
compile *and*
run a
simple C hello world program
Cheers,
Gilles
Hi,
I need some help regarding compiling
Openmpi-3.0. I have
perfectly working C compiler, however, during
configuration

/============================================================================/
/== Configuring Open MPI/

/============================================================================/
/
/
/*** Startup tests/
/checking build system type...
x86_64-unknown-linux-gnu/
/checking host system type...
x86_64-unknown-linux-gnu/
/checking target system type...
x86_64-unknown-linux-gnu/
/checking for gcc... gcc/
/checking whether the C compiler works... yes/
/checking for C compiler default output file
name...
a.out/
/checking for suffix of executables... /
/*checking whether we are cross compiling...
in `/home/user/openmpi-2.0.4':*/
/configure: error: cannot run C compiled
programs./
/If you meant to cross compile, use `--host'./
/See `config.log' for more details/
I do not know waht is cross compiling but how
can I
avoid this
error ?
Please help me out here.
Thanks
-- Abhisek Mondal
/Senior Research Fellow
/
/Structural Biology and Bioinformatics Division
/
/CSIR-Indian Institute of Chemical Biology/
/Kolkata 700032
/
/INDIA
/
_______________________________________________
users mailing list
https://lists.open-mpi.org/mailman/listinfo/users
<https://lists.open-mpi.org/mailman/listinfo/users>
<https://lists.open-mpi.org/mailman/listinfo/users
<https://lists.open-mpi.org/mailman/listinfo/users>>

<https://lists.open-mpi.org/mailman/listinfo/users
<https://lists.open-mpi.org/mailman/listinfo/users>
<https://lists.open-mpi.org/mailman/listinfo/users
<https://lists.open-mpi.org/mailman/listinfo/users>>>
_______________________________________________
users mailing list
https://lists.open-mpi.org/mailman/listinfo/users
<https://lists.open-mpi.org/mailman/listinfo/users>
<https://lists.open-mpi.org/mailman/listinfo/users
<https://lists.open-mpi.org/mailman/listinfo/users>>
<https://lists.open-mpi.org/mailman/listinfo/users
<https://lists.open-mpi.org/mailman/listinfo/users>
<https://lists.open-mpi.org/mailman/listinfo/users
<https://lists.open-mpi.org/mailman/listinfo/users>>>
-- Abhisek Mondal
/Senior Research Fellow
/
/Structural Biology and Bioinformatics Division
/
/CSIR-Indian Institute of Chemical Biology/
/Kolkata 700032
/
/INDIA
/
_______________________________________________
users mailing list
https://lists.open-mpi.org/mailman/listinfo/users
<https://lists.open-mpi.org/mailman/listinfo/users>
<https://lists.open-mpi.org/mailman/listinfo/users
<https://lists.open-mpi.org/mailman/listinfo/users>>
_______________________________________________
users mailing list
https://lists.open-mpi.org/mailman/listinfo/users
<https://lists.open-mpi.org/mailman/listinfo/users>
<https://lists.open-mpi.org/mailman/listinfo/users
<https://lists.open-mpi.org/mailman/listinfo/users>>
--
Abhisek Mondal
/Senior Research Fellow
/
/Structural Biology and Bioinformatics Division
/
/CSIR-Indian Institute of Chemical Biology/
/Kolkata 700032
/
/INDIA
/
_______________________________________________
users mailing list
https://lists.open-mpi.org/mailman/listinfo/users
<https://lists.open-mpi.org/mailman/listinfo/users>
_______________________________________________
users mailing list
https://lists.open-mpi.org/mailman/listinfo/users
<https://lists.open-mpi.org/mailman/listinfo/users>
--
Abhisek Mondal
/Senior Research Fellow
/
/Structural Biology and Bioinformatics Division
/
/CSIR-Indian Institute of Chemical Biology/
/Kolkata 700032
/
/INDIA
/
_______________________________________________
users mailing list
https://lists.open-mpi.org/mailman/listinfo/users

abhisek Mondal

2018-04-03 07:12:51 UTC

Permalink

I have cuda installed in /usr/local/cuda-8.0.

Post by Gilles Gouaillardet
Did you install CUDA and where ?

Post by abhisek Mondal
Thanks a lot. Installing the headers worked like a charm !
Version: 3.0.1
Build MPI C bindings: yes
Build MPI C++ bindings (deprecated): no
Build MPI Fortran bindings: mpif.h, use mpi
MPI Build Java bindings (experimental): no
Build Open SHMEM support: yes
Debug build: no
Platform file: (none)
Miscellaneous
-----------------------
*CUDA support: no*
*
*
*
*
I have a single GPU on my machine. Do I need to define it manually while
configuring openmpi?
It looks like kernel-headers is required too
Cheers,
Gilles
Hello,
Installing glibc moved the installation little bit but again
stuck at sanity check.
https://drive.google.com/drive/u/0/folders/0B6O-L5Y7BiGJfmQ4
N2FpblBEcFNxaDZnaGpsUFFEUlotVWFjajR0UFFHNk5aYlhoSHVTWkU
<https://drive.google.com/drive/u/0/folders/0B6O-L5Y7BiGJfmQ
4N2FpblBEcFNxaDZnaGpsUFFEUlotVWFjajR0UFFHNk5aYlhoSHVTWkU>
$ cpp --version
cpp (GCC) 4.8.5 20150623 (Red Hat 4.8.5-16)
Copyright (C) 2015 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.
There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A
PARTICULAR PURPOSE.
I have gcc and gcc-c++ installed.
On Tue, Apr 3, 2018 at 10:08 AM, Gilles Gouaillardet
This is the relevant part related to this error
configure:6620: checking whether we are cross compiling
configure:6628: gcc -o conftest conftest.c >&5
conftest.c:10:19: fatal error: stdio.h: No such file or directory
#include <stdio.h>
^
compilation terminated.
configure:6632: $? = 1
configure:6639: ./conftest
../configure: line 6641: ./conftest: No such file or directory
configure:6643: $? = 127
at the very least, you need to install the glibc-headers package
Cheers,
Gilles
Hello,
https://drive.google.com/drive/u/0/folders/0B6O-L5Y7BiGJfmQ4
N2FpblBEcFNxaDZnaGpsUFFEUlotVWFjajR0UFFHNk5aYlhoSHVTWkU
<https://drive.google.com/drive/u/0/folders/0B6O-L5Y7BiGJfmQ
4N2FpblBEcFNxaDZnaGpsUFFEUlotVWFjajR0UFFHNk5aYlhoSHVTWkU>
<https://drive.google.com/drive/u/0/folders/0B6O-L5Y7BiGJfmQ
4N2FpblBEcFNxaDZnaGpsUFFEUlotVWFjajR0UFFHNk5aYlhoSHVTWkU
<https://drive.google.com/drive/u/0/folders/0B6O-L5Y7BiGJfmQ
4N2FpblBEcFNxaDZnaGpsUFFEUlotVWFjajR0UFFHNk5aYlhoSHVTWkU>>
On Tue, Apr 3, 2018 at 9:47 AM, Gilles Gouaillardet
Can you please compress and attach your config.log ?
You might also want to double check you can
compile *and*
run a
simple C hello world program
Cheers,
Gilles
Hi,
I need some help regarding compiling
Openmpi-3.0. I have
perfectly working C compiler, however, during
configuration
/===========================================================
=================/
/== Configuring Open MPI/
/===========================================================
=================/
/
/
/*** Startup tests/
/checking build system type...
x86_64-unknown-linux-gnu/
/checking host system type...
x86_64-unknown-linux-gnu/
/checking target system type...
x86_64-unknown-linux-gnu/
/checking for gcc... gcc/
/checking whether the C compiler works... yes/
/checking for C compiler default output file
name...
a.out/
/checking for suffix of executables... /
/*checking whether we are cross compiling...
in `/home/user/openmpi-2.0.4':*/
/configure: error: cannot run C compiled programs./
/If you meant to cross compile, use `--host'./
/See `config.log' for more details/
I do not know waht is cross compiling but how can I
avoid this
error ?
Please help me out here.
Thanks
-- Abhisek Mondal
/Senior Research Fellow
/
/Structural Biology and Bioinformatics Division
/
/CSIR-Indian Institute of Chemical Biology/
/Kolkata 700032
/
/INDIA
/
_______________________________________________
users mailing list
https://lists.open-mpi.org/mailman/listinfo/users
<https://lists.open-mpi.org/mailman/listinfo/users>
<https://lists.open-mpi.org/mailman/listinfo/users
<https://lists.open-mpi.org/mailman/listinfo/users>>
<https://lists.open-mpi.org/mailman/listinfo/users
<https://lists.open-mpi.org/mailman/listinfo/users>
<https://lists.open-mpi.org/mailman/listinfo/users
<https://lists.open-mpi.org/mailman/listinfo/users>>>
_______________________________________________
users mailing list
https://lists.open-mpi.org/mailman/listinfo/users
<https://lists.open-mpi.org/mailman/listinfo/users>
<https://lists.open-mpi.org/mailman/listinfo/users
<https://lists.open-mpi.org/mailman/listinfo/users>>
<https://lists.open-mpi.org/mailman/listinfo/users
<https://lists.open-mpi.org/mailman/listinfo/users>
<https://lists.open-mpi.org/mailman/listinfo/users
<https://lists.open-mpi.org/mailman/listinfo/users>>>
-- Abhisek Mondal
/Senior Research Fellow
/
/Structural Biology and Bioinformatics Division
/
/CSIR-Indian Institute of Chemical Biology/
/Kolkata 700032
/
/INDIA
/
_______________________________________________
users mailing list
https://lists.open-mpi.org/mailman/listinfo/users
<https://lists.open-mpi.org/mailman/listinfo/users>
<https://lists.open-mpi.org/mailman/listinfo/users
<https://lists.open-mpi.org/mailman/listinfo/users>>
_______________________________________________
users mailing list
https://lists.open-mpi.org/mailman/listinfo/users
<https://lists.open-mpi.org/mailman/listinfo/users>
<https://lists.open-mpi.org/mailman/listinfo/users
<https://lists.open-mpi.org/mailman/listinfo/users>>
-- Abhisek Mondal
/Senior Research Fellow
/
/Structural Biology and Bioinformatics Division
/
/CSIR-Indian Institute of Chemical Biology/
/Kolkata 700032
/
/INDIA
/
_______________________________________________
users mailing list
https://lists.open-mpi.org/mailman/listinfo/users
<https://lists.open-mpi.org/mailman/listinfo/users>
_______________________________________________
users mailing list
https://lists.open-mpi.org/mailman/listinfo/users
<https://lists.open-mpi.org/mailman/listinfo/users>
--
Abhisek Mondal
/Senior Research Fellow
/
/Structural Biology and Bioinformatics Division
/
/CSIR-Indian Institute of Chemical Biology/
/Kolkata 700032
/
/INDIA
/
_______________________________________________
users mailing list
https://lists.open-mpi.org/mailman/listinfo/users

_______________________________________________
users mailing list
https://lists.open-mpi.org/mailman/listinfo/users

--
Abhisek Mondal

*Senior Research Fellow*

*Structural Biology and Bioinformatics Division*
*CSIR-Indian Institute of Chemical Biology*

*Kolkata 700032*

*INDIA*

Gilles Gouaillardet

2018-04-03 07:24:46 UTC

Permalink

In that case, you need to

configure --with-cuda=/usr/local/cuda-8.0

Cheers,

Gilles

Post by abhisek Mondal
I have cuda installed in /usr/local/cuda-8.0.
On Tue, Apr 3, 2018 at 12:37 PM, Gilles Gouaillardet
Did you install CUDA and where ?
Thanks a lot. Installing the headers worked like a charm !
Version: 3.0.1
Build MPI C bindings: yes
Build MPI C++ bindings (deprecated): no
Build MPI Fortran bindings: mpif.h, use mpi
MPI Build Java bindings (experimental): no
Build Open SHMEM support: yes
Debug build: no
Platform file: (none)
Miscellaneous
-----------------------
*CUDA support: no*
*
*
*
*
I have a single GPU on my machine. Do I need to define it
manually while configuring openmpi?
On Tue, Apr 3, 2018 at 11:21 AM, Gilles Gouaillardet
It looks like kernel-headers is required too
Cheers,
Gilles
Hello,
Installing glibc moved the installation little bit but
again
stuck at sanity check.
https://drive.google.com/drive/u/0/folders/0B6O-L5Y7BiGJfmQ4N2FpblBEcFNxaDZnaGpsUFFEUlotVWFjajR0UFFHNk5aYlhoSHVTWkU
<https://drive.google.com/drive/u/0/folders/0B6O-L5Y7BiGJfmQ4N2FpblBEcFNxaDZnaGpsUFFEUlotVWFjajR0UFFHNk5aYlhoSHVTWkU>

<https://drive.google.com/drive/u/0/folders/0B6O-L5Y7BiGJfmQ4N2FpblBEcFNxaDZnaGpsUFFEUlotVWFjajR0UFFHNk5aYlhoSHVTWkU
<https://drive.google.com/drive/u/0/folders/0B6O-L5Y7BiGJfmQ4N2FpblBEcFNxaDZnaGpsUFFEUlotVWFjajR0UFFHNk5aYlhoSHVTWkU>>
$ cpp --version
cpp (GCC) 4.8.5 20150623 (Red Hat 4.8.5-16)
Copyright (C) 2015 Free Software Foundation, Inc.
This is free software; see the source for copying
conditions.
There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A
PARTICULAR PURPOSE.
I have gcc and gcc-c++ installed.
On Tue, Apr 3, 2018 at 10:08 AM, Gilles Gouaillardet
This is the relevant part related to this error
configure:6620: checking whether we are cross
compiling
configure:6628: gcc -o conftest conftest.c >&5
conftest.c:10:19: fatal error: stdio.h: No such
file or
directory
#include <stdio.h>
^
compilation terminated.
configure:6632: $? = 1
configure:6639: ./conftest
../configure: line 6641: ./conftest: No such file
or directory
configure:6643: $? = 127
at the very least, you need to install the
glibc-headers
package
Cheers,
Gilles
Hello,
https://drive.google.com/drive/u/0/folders/0B6O-L5Y7BiGJfmQ4N2FpblBEcFNxaDZnaGpsUFFEUlotVWFjajR0UFFHNk5aYlhoSHVTWkU
<https://drive.google.com/drive/u/0/folders/0B6O-L5Y7BiGJfmQ4N2FpblBEcFNxaDZnaGpsUFFEUlotVWFjajR0UFFHNk5aYlhoSHVTWkU>

<https://drive.google.com/drive/u/0/folders/0B6O-L5Y7BiGJfmQ4N2FpblBEcFNxaDZnaGpsUFFEUlotVWFjajR0UFFHNk5aYlhoSHVTWkU
<https://drive.google.com/drive/u/0/folders/0B6O-L5Y7BiGJfmQ4N2FpblBEcFNxaDZnaGpsUFFEUlotVWFjajR0UFFHNk5aYlhoSHVTWkU>>

<https://drive.google.com/drive/u/0/folders/0B6O-L5Y7BiGJfmQ4N2FpblBEcFNxaDZnaGpsUFFEUlotVWFjajR0UFFHNk5aYlhoSHVTWkU
<https://drive.google.com/drive/u/0/folders/0B6O-L5Y7BiGJfmQ4N2FpblBEcFNxaDZnaGpsUFFEUlotVWFjajR0UFFHNk5aYlhoSHVTWkU>

<https://drive.google.com/drive/u/0/folders/0B6O-L5Y7BiGJfmQ4N2FpblBEcFNxaDZnaGpsUFFEUlotVWFjajR0UFFHNk5aYlhoSHVTWkU
<https://drive.google.com/drive/u/0/folders/0B6O-L5Y7BiGJfmQ4N2FpblBEcFNxaDZnaGpsUFFEUlotVWFjajR0UFFHNk5aYlhoSHVTWkU>>>
On Tue, Apr 3, 2018 at 9:47 AM, Gilles
Gouaillardet
Can you please compress and attach your
config.log ?
You might also want to double check you can
compile *and*
run a
simple C hello world program
Cheers,
Gilles
Hi,
I need some help regarding compiling
Openmpi-3.0. I have
perfectly working C compiler, however,
during
configuration

/============================================================================/
/== Configuring Open MPI/

/============================================================================/
/
/
/*** Startup tests/
/checking build system type...
x86_64-unknown-linux-gnu/
/checking host system type...
x86_64-unknown-linux-gnu/
/checking target system type...
x86_64-unknown-linux-gnu/
/checking for gcc... gcc/
/checking whether the C compiler
works... yes/
/checking for C compiler default
output file
name...
a.out/
/checking for suffix of executables... /
/*checking whether we are cross
compiling...
in `/home/user/openmpi-2.0.4':*/
/configure: error: cannot run C compiled
programs./
/If you meant to cross compile, use
`--host'./
/See `config.log' for more details/
I do not know waht is cross compiling
but how
can I
avoid this
error ?
Please help me out here.
Thanks
-- Abhisek Mondal
/Senior Research Fellow
/
/Structural Biology and Bioinformatics
Division
/
/CSIR-Indian Institute of Chemical
Biology/
/Kolkata 700032
/
/INDIA
/

_______________________________________________
users mailing list
https://lists.open-mpi.org/mailman/listinfo/users
<https://lists.open-mpi.org/mailman/listinfo/users>
<https://lists.open-mpi.org/mailman/listinfo/users
<https://lists.open-mpi.org/mailman/listinfo/users>>

<https://lists.open-mpi.org/mailman/listinfo/users
<https://lists.open-mpi.org/mailman/listinfo/users>
<https://lists.open-mpi.org/mailman/listinfo/users
<https://lists.open-mpi.org/mailman/listinfo/users>>>
<https://lists.open-mpi.org/mailman/listinfo/users
<https://lists.open-mpi.org/mailman/listinfo/users>
<https://lists.open-mpi.org/mailman/listinfo/users
<https://lists.open-mpi.org/mailman/listinfo/users>>

<https://lists.open-mpi.org/mailman/listinfo/users
<https://lists.open-mpi.org/mailman/listinfo/users>
<https://lists.open-mpi.org/mailman/listinfo/users
<https://lists.open-mpi.org/mailman/listinfo/users>>>>

_______________________________________________
users mailing list
https://lists.open-mpi.org/mailman/listinfo/users
<https://lists.open-mpi.org/mailman/listinfo/users>
<https://lists.open-mpi.org/mailman/listinfo/users
<https://lists.open-mpi.org/mailman/listinfo/users>>

<https://lists.open-mpi.org/mailman/listinfo/users
<https://lists.open-mpi.org/mailman/listinfo/users>
<https://lists.open-mpi.org/mailman/listinfo/users
<https://lists.open-mpi.org/mailman/listinfo/users>>>

<https://lists.open-mpi.org/mailman/listinfo/users
<https://lists.open-mpi.org/mailman/listinfo/users>
<https://lists.open-mpi.org/mailman/listinfo/users
<https://lists.open-mpi.org/mailman/listinfo/users>>

<https://lists.open-mpi.org/mailman/listinfo/users
<https://lists.open-mpi.org/mailman/listinfo/users>
<https://lists.open-mpi.org/mailman/listinfo/users
<https://lists.open-mpi.org/mailman/listinfo/users>>>>
-- Abhisek Mondal
/Senior Research Fellow
/
/Structural Biology and Bioinformatics Division
/
/CSIR-Indian Institute of Chemical Biology/
/Kolkata 700032
/
/INDIA
/
_______________________________________________
users mailing list
https://lists.open-mpi.org/mailman/listinfo/users
<https://lists.open-mpi.org/mailman/listinfo/users>
<https://lists.open-mpi.org/mailman/listinfo/users
<https://lists.open-mpi.org/mailman/listinfo/users>>

<https://lists.open-mpi.org/mailman/listinfo/users
<https://lists.open-mpi.org/mailman/listinfo/users>
<https://lists.open-mpi.org/mailman/listinfo/users
<https://lists.open-mpi.org/mailman/listinfo/users>>>
_______________________________________________
users mailing list
https://lists.open-mpi.org/mailman/listinfo/users
<https://lists.open-mpi.org/mailman/listinfo/users>
<https://lists.open-mpi.org/mailman/listinfo/users
<https://lists.open-mpi.org/mailman/listinfo/users>>
<https://lists.open-mpi.org/mailman/listinfo/users
<https://lists.open-mpi.org/mailman/listinfo/users>
<https://lists.open-mpi.org/mailman/listinfo/users
<https://lists.open-mpi.org/mailman/listinfo/users>>>
-- Abhisek Mondal
/Senior Research Fellow
/
/Structural Biology and Bioinformatics Division
/
/CSIR-Indian Institute of Chemical Biology/
/Kolkata 700032
/
/INDIA
/
_______________________________________________
users mailing list
https://lists.open-mpi.org/mailman/listinfo/users
<https://lists.open-mpi.org/mailman/listinfo/users>
<https://lists.open-mpi.org/mailman/listinfo/users
<https://lists.open-mpi.org/mailman/listinfo/users>>
_______________________________________________
users mailing list
https://lists.open-mpi.org/mailman/listinfo/users
<https://lists.open-mpi.org/mailman/listinfo/users>
<https://lists.open-mpi.org/mailman/listinfo/users
<https://lists.open-mpi.org/mailman/listinfo/users>>
--
Abhisek Mondal
/Senior Research Fellow
/
/Structural Biology and Bioinformatics Division
/
/CSIR-Indian Institute of Chemical Biology/
/Kolkata 700032
/
/INDIA
/
_______________________________________________
users mailing list
https://lists.open-mpi.org/mailman/listinfo/users
<https://lists.open-mpi.org/mailman/listinfo/users>
_______________________________________________
users mailing list
https://lists.open-mpi.org/mailman/listinfo/users
<https://lists.open-mpi.org/mailman/listinfo/users>
--
Abhisek Mondal
/Senior Research Fellow
/
/Structural Biology and Bioinformatics Division
/
/CSIR-Indian Institute of Chemical Biology/
/Kolkata 700032
/
/INDIA
/
_______________________________________________
users mailing list
https://lists.open-mpi.org/mailman/listinfo/users

abhisek Mondal

2018-04-03 08:23:31 UTC

Permalink

Thanks a lot.
It worked very nicely for me.

Post by Gilles Gouaillardet
In that case, you need to
configure --with-cuda=/usr/local/cuda-8.0
Cheers,
Gilles

Post by abhisek Mondal
I have cuda installed in /usr/local/cuda-8.0.
Did you install CUDA and where ?
Thanks a lot. Installing the headers worked like a charm !
Version: 3.0.1
Build MPI C bindings: yes
Build MPI C++ bindings (deprecated): no
Build MPI Fortran bindings: mpif.h, use mpi
MPI Build Java bindings (experimental): no
Build Open SHMEM support: yes
Debug build: no
Platform file: (none)
Miscellaneous
-----------------------
*CUDA support: no*
*
*
*
*
I have a single GPU on my machine. Do I need to define it
manually while configuring openmpi?
On Tue, Apr 3, 2018 at 11:21 AM, Gilles Gouaillardet
It looks like kernel-headers is required too
Cheers,
Gilles
Hello,
Installing glibc moved the installation little bit but again
stuck at sanity check.
https://drive.google.com/drive/u/0/folders/0B6O-L5Y7BiGJfmQ4
N2FpblBEcFNxaDZnaGpsUFFEUlotVWFjajR0UFFHNk5aYlhoSHVTWkU
<https://drive.google.com/drive/u/0/folders/0B6O-L5Y7BiGJfmQ
4N2FpblBEcFNxaDZnaGpsUFFEUlotVWFjajR0UFFHNk5aYlhoSHVTWkU>
<https://drive.google.com/drive/u/0/folders/0B6O-L5Y7BiGJfmQ
4N2FpblBEcFNxaDZnaGpsUFFEUlotVWFjajR0UFFHNk5aYlhoSHVTWkU
<https://drive.google.com/drive/u/0/folders/0B6O-L5Y7BiGJfmQ
4N2FpblBEcFNxaDZnaGpsUFFEUlotVWFjajR0UFFHNk5aYlhoSHVTWkU>>
$ cpp --version
cpp (GCC) 4.8.5 20150623 (Red Hat 4.8.5-16)
Copyright (C) 2015 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.
There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A
PARTICULAR PURPOSE.
I have gcc and gcc-c++ installed.
On Tue, Apr 3, 2018 at 10:08 AM, Gilles Gouaillardet
This is the relevant part related to this error
configure:6620: checking whether we are cross compiling
configure:6628: gcc -o conftest conftest.c >&5
conftest.c:10:19: fatal error: stdio.h: No such
file or
directory
#include <stdio.h>
^
compilation terminated.
configure:6632: $? = 1
configure:6639: ./conftest
../configure: line 6641: ./conftest: No such file
or directory
configure:6643: $? = 127
at the very least, you need to install the
glibc-headers
package
Cheers,
Gilles
Hello,
https://drive.google.com/drive/u/0/folders/0B6O-L5Y7BiGJfmQ4
N2FpblBEcFNxaDZnaGpsUFFEUlotVWFjajR0UFFHNk5aYlhoSHVTWkU
<https://drive.google.com/drive/u/0/folders/0B6O-L5Y7BiGJfmQ
4N2FpblBEcFNxaDZnaGpsUFFEUlotVWFjajR0UFFHNk5aYlhoSHVTWkU>
<https://drive.google.com/drive/u/0/folders/0B6O-L5Y7BiGJfmQ
4N2FpblBEcFNxaDZnaGpsUFFEUlotVWFjajR0UFFHNk5aYlhoSHVTWkU
<https://drive.google.com/drive/u/0/folders/0B6O-L5Y7BiGJfmQ
4N2FpblBEcFNxaDZnaGpsUFFEUlotVWFjajR0UFFHNk5aYlhoSHVTWkU>>
<https://drive.google.com/drive/u/0/folders/0B6O-L5Y7BiGJfmQ
4N2FpblBEcFNxaDZnaGpsUFFEUlotVWFjajR0UFFHNk5aYlhoSHVTWkU
<https://drive.google.com/drive/u/0/folders/0B6O-L5Y7BiGJfmQ
4N2FpblBEcFNxaDZnaGpsUFFEUlotVWFjajR0UFFHNk5aYlhoSHVTWkU>
<https://drive.google.com/drive/u/0/folders/0B6O-L5Y7BiGJfmQ
4N2FpblBEcFNxaDZnaGpsUFFEUlotVWFjajR0UFFHNk5aYlhoSHVTWkU
<https://drive.google.com/drive/u/0/folders/0B6O-L5Y7BiGJfmQ
4N2FpblBEcFNxaDZnaGpsUFFEUlotVWFjajR0UFFHNk5aYlhoSHVTWkU>>>
On Tue, Apr 3, 2018 at 9:47 AM, Gilles Gouaillardet
Can you please compress and attach your config.log ?
You might also want to double check you can
compile *and*
run a
simple C hello world program
Cheers,
Gilles
Hi,
I need some help regarding compiling
Openmpi-3.0. I have
perfectly working C compiler, however, during
configuration
/===========================================================
=================/
/== Configuring Open MPI/
/===========================================================
=================/
/
/
/*** Startup tests/
/checking build system type...
x86_64-unknown-linux-gnu/
/checking host system type...
x86_64-unknown-linux-gnu/
/checking target system type...
x86_64-unknown-linux-gnu/
/checking for gcc... gcc/
/checking whether the C compiler works... yes/
/checking for C compiler default output file
name...
a.out/
/checking for suffix of executables... /
/*checking whether we are cross compiling...
in `/home/user/openmpi-2.0.4':*/
/configure: error: cannot run C compiled
programs./
/If you meant to cross compile, use `--host'./
/See `config.log' for more details/
I do not know waht is cross compiling
but how
can I
avoid this
error ?
Please help me out here.
Thanks
-- Abhisek Mondal
/Senior Research Fellow
/
/Structural Biology and Bioinformatics Division
/
/CSIR-Indian Institute of Chemical Biology/
/Kolkata 700032
/
/INDIA
/
_______________________________________________
users mailing list
https://lists.open-mpi.org/mailman/listinfo/users
<https://lists.open-mpi.org/mailman/listinfo/users>
<https://lists.open-mpi.org/mailman/listinfo/users
<https://lists.open-mpi.org/mailman/listinfo/users>>
<https://lists.open-mpi.org/mailman/listinfo/users
<https://lists.open-mpi.org/mailman/listinfo/users>
<https://lists.open-mpi.org/mailman/listinfo/users
<https://lists.open-mpi.org/mailman/listinfo/users>>>
<https://lists.open-mpi.org/mailman/listinfo/users
<https://lists.open-mpi.org/mailman/listinfo/users>
<https://lists.open-mpi.org/mailman/listinfo/users
<https://lists.open-mpi.org/mailman/listinfo/users>>
<https://lists.open-mpi.org/mailman/listinfo/users
<https://lists.open-mpi.org/mailman/listinfo/users>
<https://lists.open-mpi.org/mailman/listinfo/users
<https://lists.open-mpi.org/mailman/listinfo/users>>>>
_______________________________________________
users mailing list
https://lists.open-mpi.org/mailman/listinfo/users
<https://lists.open-mpi.org/mailman/listinfo/users>
<https://lists.open-mpi.org/mailman/listinfo/users
<https://lists.open-mpi.org/mailman/listinfo/users>>
<https://lists.open-mpi.org/mailman/listinfo/users
<https://lists.open-mpi.org/mailman/listinfo/users>
<https://lists.open-mpi.org/mailman/listinfo/users
<https://lists.open-mpi.org/mailman/listinfo/users>>>
<https://lists.open-mpi.org/mailman/listinfo/users
<https://lists.open-mpi.org/mailman/listinfo/users>
<https://lists.open-mpi.org/mailman/listinfo/users
<https://lists.open-mpi.org/mailman/listinfo/users>>
<https://lists.open-mpi.org/mailman/listinfo/users
<https://lists.open-mpi.org/mailman/listinfo/users>
<https://lists.open-mpi.org/mailman/listinfo/users
<https://lists.open-mpi.org/mailman/listinfo/users>>>>
-- Abhisek Mondal
/Senior Research Fellow
/
/Structural Biology and Bioinformatics Division
/
/CSIR-Indian Institute of Chemical Biology/
/Kolkata 700032
/
/INDIA
/
_______________________________________________
users mailing list
https://lists.open-mpi.org/mailman/listinfo/users
<https://lists.open-mpi.org/mailman/listinfo/users>
<https://lists.open-mpi.org/mailman/listinfo/users
<https://lists.open-mpi.org/mailman/listinfo/users>>
<https://lists.open-mpi.org/mailman/listinfo/users
<https://lists.open-mpi.org/mailman/listinfo/users>
<https://lists.open-mpi.org/mailman/listinfo/users
<https://lists.open-mpi.org/mailman/listinfo/users>>>
_______________________________________________
users mailing list
https://lists.open-mpi.org/mailman/listinfo/users
<https://lists.open-mpi.org/mailman/listinfo/users>
<https://lists.open-mpi.org/mailman/listinfo/users
<https://lists.open-mpi.org/mailman/listinfo/users>>
<https://lists.open-mpi.org/mailman/listinfo/users
<https://lists.open-mpi.org/mailman/listinfo/users>
<https://lists.open-mpi.org/mailman/listinfo/users
<https://lists.open-mpi.org/mailman/listinfo/users>>>
-- Abhisek Mondal
/Senior Research Fellow
/
/Structural Biology and Bioinformatics Division
/
/CSIR-Indian Institute of Chemical Biology/
/Kolkata 700032
/
/INDIA
/
_______________________________________________
users mailing list
https://lists.open-mpi.org/mailman/listinfo/users
<https://lists.open-mpi.org/mailman/listinfo/users>
<https://lists.open-mpi.org/mailman/listinfo/users
<https://lists.open-mpi.org/mailman/listinfo/users>>
_______________________________________________
users mailing list
https://lists.open-mpi.org/mailman/listinfo/users
<https://lists.open-mpi.org/mailman/listinfo/users>
<https://lists.open-mpi.org/mailman/listinfo/users
<https://lists.open-mpi.org/mailman/listinfo/users>>
-- Abhisek Mondal
/Senior Research Fellow
/
/Structural Biology and Bioinformatics Division
/
/CSIR-Indian Institute of Chemical Biology/
/Kolkata 700032
/
/INDIA
/
_______________________________________________
users mailing list
https://lists.open-mpi.org/mailman/listinfo/users
<https://lists.open-mpi.org/mailman/listinfo/users>
_______________________________________________
users mailing list
https://lists.open-mpi.org/mailman/listinfo/users
<https://lists.open-mpi.org/mailman/listinfo/users>
--
Abhisek Mondal
/Senior Research Fellow
/
/Structural Biology and Bioinformatics Division
/
/CSIR-Indian Institute of Chemical Biology/
/Kolkata 700032
/
/INDIA
/
_______________________________________________
users mailing list
https://lists.open-mpi.org/mailman/listinfo/users

_______________________________________________
users mailing list
https://lists.open-mpi.org/mailman/listinfo/users

--
Abhisek Mondal

*Senior Research Fellow*

*Structural Biology and Bioinformatics Division*
*CSIR-Indian Institute of Chemical Biology*

*Kolkata 700032*

*INDIA*

Douglas L Reeder

2018-04-03 04:18:34 UTC

Permalink

In the boldface line it refers to an openmpi-2.0.4 installation. It appears that the 3.0 build is trying to use libraires or includes from the 2.04 install instead of the 3.0 build. Can you carefully define your PATH and LD_LIBRARY_PATH (or whatever linux calls it) to prevent the 3.0 build from accessing the 2.04 build libraries and includes (modules is another way to accomplish this).

Doug

Post by abhisek Mondal
Hi,
============================================================================
== Configuring Open MPI
============================================================================
*** Startup tests
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking target system type... x86_64-unknown-linux-gnu
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
configure: error: cannot run C compiled programs.
If you meant to cross compile, use `--host'.
See `config.log' for more details
I do not know waht is cross compiling but how can I avoid this error ?
Please help me out here.
Thanks
--
Abhisek Mondal
Senior Research Fellow
Structural Biology and Bioinformatics Division
CSIR-Indian Institute of Chemical Biology
Kolkata 700032
INDIA
_______________________________________________
users mailing list
https://lists.open-mpi.org/mailman/listinfo/users

abhisek Mondal

2018-04-03 04:28:26 UTC

Permalink

Actually this error is happening for both versions. I tried to build
openmpi-2.0 and openmpi-3.0.

Post by Douglas L Reeder
In the boldface line it refers to an openmpi-2.0.4 installation. It
appears that the 3.0 build is trying to use libraires or includes from the
2.04 install instead of the 3.0 build. Can you carefully define your PATH
and LD_LIBRARY_PATH (or whatever linux calls it) to prevent the 3.0 build
from accessing the 2.04 build libraries and includes (modules is another
way to accomplish this).
Doug
Hi,
I need some help regarding compiling Openmpi-3.0. I have perfectly working
*============================================================================*
*== Configuring Open MPI*
*============================================================================*
**** Startup tests*
*checking build system type... x86_64-unknown-linux-gnu*
*checking host system type... x86_64-unknown-linux-gnu*
*checking target system type... x86_64-unknown-linux-gnu*
*checking for gcc... gcc*
*checking whether the C compiler works... yes*
*checking for C compiler default output file name... a.out*
*checking for suffix of executables... *
*checking whether we are cross compiling... configure: error: in
`/home/user/openmpi-2.0.4':*
*configure: error: cannot run C compiled programs.*
*If you meant to cross compile, use `--host'.*
*See `config.log' for more details*
I do not know waht is cross compiling but how can I avoid this error ?
Please help me out here.
Thanks
--
Abhisek Mondal
*Senior Research Fellow*
*Structural Biology and Bioinformatics Division*
*CSIR-Indian Institute of Chemical Biology*
*Kolkata 700032*
*INDIA*
_______________________________________________
users mailing list
https://lists.open-mpi.org/mailman/listinfo/users
_______________________________________________
users mailing list
https://lists.open-mpi.org/mailman/listinfo/users

--
Abhisek Mondal

*Senior Research Fellow*

*Structural Biology and Bioinformatics Division*
*CSIR-Indian Institute of Chemical Biology*

*Kolkata 700032*

*INDIA*

abhisek Mondal

2018-04-03 04:33:24 UTC

Permalink

To be accurate, the error is:

[***@localhost build]# ../configure --prefix=/usr/local/openmpi-3.0
checking for perl... perl

============================================================================
== Configuring Open MPI
============================================================================

*** Startup tests
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking target system type... x86_64-unknown-linux-gnu
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
*checking whether we are cross compiling... configure: error: in
`/home/user/openmpi-3.0.1/build':*
configure: error: cannot run C compiled programs.
If you meant to cross compile, use `--host'.
See `config.log' for more details

I had installed openmpi-3.0 before and removed it for some reason. While
reinstalling I'm getting this error. Is there any thing left during
removing older installation that is creating problem ?

Post by abhisek Mondal
Actually this error is happening for both versions. I tried to build
openmpi-2.0 and openmpi-3.0.

Post by Douglas L Reeder
In the boldface line it refers to an openmpi-2.0.4 installation. It
appears that the 3.0 build is trying to use libraires or includes from the
2.04 install instead of the 3.0 build. Can you carefully define your PATH
and LD_LIBRARY_PATH (or whatever linux calls it) to prevent the 3.0 build
from accessing the 2.04 build libraries and includes (modules is another
way to accomplish this).
Doug
Hi,
I need some help regarding compiling Openmpi-3.0. I have perfectly
working C compiler, however, during configuration I'm keep getting this
*============================================================================*
*== Configuring Open MPI*
*============================================================================*
**** Startup tests*
*checking build system type... x86_64-unknown-linux-gnu*
*checking host system type... x86_64-unknown-linux-gnu*
*checking target system type... x86_64-unknown-linux-gnu*
*checking for gcc... gcc*
*checking whether the C compiler works... yes*
*checking for C compiler default output file name... a.out*
*checking for suffix of executables... *
*checking whether we are cross compiling... configure: error: in
`/home/user/openmpi-2.0.4':*
*configure: error: cannot run C compiled programs.*
*If you meant to cross compile, use `--host'.*
*See `config.log' for more details*
I do not know waht is cross compiling but how can I avoid this error ?
Please help me out here.
Thanks
--
Abhisek Mondal
*Senior Research Fellow*
*Structural Biology and Bioinformatics Division*
*CSIR-Indian Institute of Chemical Biology*
*Kolkata 700032*
*INDIA*
_______________________________________________
users mailing list
https://lists.open-mpi.org/mailman/listinfo/users
_______________________________________________
users mailing list
https://lists.open-mpi.org/mailman/listinfo/users

--
Abhisek Mondal
*Senior Research Fellow*
*Structural Biology and Bioinformatics Division*
*CSIR-Indian Institute of Chemical Biology*
*Kolkata 700032*
*INDIA*

--
Abhisek Mondal

*Senior Research Fellow*

*Structural Biology and Bioinformatics Division*
*CSIR-Indian Institute of Chemical Biology*

*Kolkata 700032*

*INDIA*