[OMPI users] Fwd: Make All error regarding either "Conflicting" or "Previous Declaration" among others

[Aragorn Inocencio]

Good evening,

Thank you for taking the time to develop and assist in the use of this tool.

I am trying to install the latest mpich-3.2 version to run Reef3D and my
current setup is as follows (sorry I don't know which data is relevant so
I'm including as much as possible):


- Windows 7 Professional SP 1
- Installed cygwin using the instructions from the Reef3D manual
- C compiler previously installed on my laptop is Dev C++ 5.8.2, with
the Compiler Options saying "Compiler set to configure" "TDM-GCC 4.8.1
64-bit Release"
- echo $shell throws me "/bin/bash"

So I have successfully done the configure step (step d) in the readme, but
running the make command gives me various errors such as:

- error: redefinition of ‘struct hostent’
- arning: #warning "fd_set and associated macros have been defined in
sys/types. This can cause runtime problems with W32 sockets" [-Wcpp]
- /usr/include/w32api/winsock2.h:976:34: error: conflicting types for
‘connect’

etc. The main logs are attached for reference as instructed in the readme;
however I could not find mpich-3.2/src/pm/hydra/
tools/topo/hwloc/hwloc/config.log in the designated folder. The mv.txt is
the output for when running the make V=1 command, so I didn't overwrite the
previous m.txt

Much appreciated.

[r***@open-mpi.org]

Err...you might want to ask the MPICH folks. This is the Open MPI mailing list :-)

Post by Aragorn Inocencio
Good evening,
Thank you for taking the time to develop and assist in the use of this tool.
Windows 7 Professional SP 1
Installed cygwin using the instructions from the Reef3D manual
C compiler previously installed on my laptop is Dev C++ 5.8.2, with the Compiler Options saying "Compiler set to configure" "TDM-GCC 4.8.1 64-bit Release"
echo $shell throws me "/bin/bash"
error: redefinition of ‘struct hostent’
arning: #warning "fd_set and associated macros have been defined in sys/types. This can cause runtime problems with W32 sockets" [-Wcpp]
/usr/include/w32api/winsock2.h:976:34: error: conflicting types for ‘connect’
etc. The main logs are attached for reference as instructed in the readme; however I could not find mpich-3.2/src/pm/hydra/tools/topo/hwloc/hwloc/config.log in the designated folder. The mv.txt is the output for when running the make V=1 command, so I didn't overwrite the previous m.txt
Much appreciated.
--
Ismael Aragorn D. Inocencio
Civil Engineer
--
Ismael Aragorn D. Inocencio
Civil Engineer
<src error logs.zip><main error logs.zip>_______________________________________________
users mailing list
https://lists.open-mpi.org/mailman/listinfo/users

[Aragorn Inocencio]

. . . My sincerest apologies, I have gotten utterly mixed up; this is all
new territory for me.

Post by r***@open-mpi.org
Err...you might want to ask the MPICH folks. This is the Open MPI mailing list :-)
On Sep 19, 2017, at 7:38 AM, Aragorn Inocencio <
Good evening,
Thank you for taking the time to develop and assist in the use of this tool.
I am trying to install the latest mpich-3.2 version to run Reef3D and my
current setup is as follows (sorry I don't know which data is relevant so
- Windows 7 Professional SP 1
- Installed cygwin using the instructions from the Reef3D manual
- C compiler previously installed on my laptop is Dev C++ 5.8.2, with
the Compiler Options saying "Compiler set to configure" "TDM-GCC 4.8.1
64-bit Release"
- echo $shell throws me "/bin/bash"
So I have successfully done the configure step (step d) in the readme, but
- error: redefinition of ‘struct hostent’
- arning: #warning "fd_set and associated macros have been defined in
sys/types. This can cause runtime problems with W32 sockets" [-Wcpp]
- /usr/include/w32api/winsock2.h:976:34: error: conflicting types for
‘connect’
etc. The main logs are attached for reference as instructed in the readme;
however I could not find mpich-3.2/src/pm/hydra/to
ols/topo/hwloc/hwloc/config.log in the designated folder. The mv.txt is
the output for when running the make V=1 command, so I didn't overwrite the
previous m.txt
Much appreciated.
--
Ismael Aragorn D. Inocencio
Civil Engineer
--
Ismael Aragorn D. Inocencio
Civil Engineer
<src error logs.zip><main error logs.zip>_____________________
__________________________
users mailing list
https://lists.open-mpi.org/mailman/listinfo/users
_______________________________________________
users mailing list
https://lists.open-mpi.org/mailman/listinfo/users

[Aragorn Inocencio]

Hi, sorry about the mixup earlier. But I have recently tried installing
openmpi 3.0.0 using the instructions I found in the Reef3D manual (attached
below), so

./configure CC=gcc CXX=g++ F77=gfortran FC=gfortran
--prefix=/usr/local/openmpi

throws no errors, but again when I run the "make all" command next I am
getting quite a few errors, to name a few:


1. #warning "fd_set and associated macros have been defined in sys/types
2. error: redefinition of struct hostent
3. A bunch of other errors similar to 2
4. A bunch of errors saying, "conflicting types for 'accept' bind,
connect etc.
5. "Expected declaration specifiers or '...' before '("
6. previous declaration of various functions

then all the way at the end it gives me an Error 1.

I'd like to apologize for my ignorance as I really have no background in
this area; I don't even know how to print all the errors to a txt file.
For what it's worth I have attached the config.log file.

​[image: Inline image 1]

[Jeff Squyres (jsquyres)]

Hi, sorry about the mixup earlier. But I have recently tried installing openmpi 3.0.0 using the instructions I found in the Reef3D manual (attached below), so
./configure CC=gcc CXX=g++ F77=gfortran FC=gfortran --prefix=/usr/local/openmpi
• #warning "fd_set and associated macros have been defined in sys/types
• error: redefinition of struct hostent
• A bunch of other errors similar to 2
• A bunch of errors saying, "conflicting types for 'accept' bind, connect etc.
• "Expected declaration specifiers or '...' before '("
• previous declaration of various functions
then all the way at the end it gives me an Error 1.
I'd like to apologize for my ignorance as I really have no background in this area; I don't even know how to print all the errors to a txt file. For what it's worth I have attached the config.log file.

No worries; we're here to help.

If you're getting build errors, we'll need to see your build logs. See https://www.open-mpi.org/community/help/ for some help gathering the information we'll need.

Is this still on Windows, or is this on Linux?

Open MPI unfortunately no longer supports Windows -- if you're getting build errors on Windows, that might be expected (since we haven't tried to build on Windows in ... a long time).

--
Jeff Squyres
***@cisco.com

[Gus Correa]

Hi, sorry about the mixup earlier.  But I have recently tried installing
openmpi 3.0.0 using the instructions I found in the Reef3D manual
(attached below), so
./configure CC=gcc CXX=g++ F77=gfortran FC=gfortran
--prefix=/usr/local/openmpi
throws no errors, but again when I run the "make all" command next I am
1. #warning "fd_set and associated macros have been defined in sys/types
2. error: redefinition of struct hostent
3. A bunch of other errors similar to 2
4. A bunch of errors saying, "conflicting types for 'accept' bind,
connect etc.
5. "Expected declaration specifiers or '...' before '("
6. previous declaration of various functions
then all the way at the end it gives me an Error 1.
I'd like to apologize for my ignorance as I really have no background in
this area; I don't even know how to print all the errors to a txt file.

** If using sh/bash:

./configure CC=gcc CXX=g++ F77=gfortran FC=gfortran
--prefix=/usr/local/openmpi 2>&1 | tee my_configure.log

make 2>&1 | tee my_make.log

make install 2>&1 | tee my_make_install.log

** If using csh/tcsh:

./configure CC=gcc CXX=g++ F77=gfortran FC=gfortran
--prefix=/usr/local/openmpi |& tee my_configure.log

make |& tee my_make.log

make install |& tee my_make_install.log

I hope this helps,
Gus Correa

For what it's worth I have attached the config.log file.
​Inline image 1
_______________________________________________
users mailing list
https://lists.open-mpi.org/mailman/listinfo/users

[Aragorn Inocencio]

Good morning,

Thanks for the input Jeff; yes I am still doing this in Windows via cygwin.
I currently do not have a Linux machine.

Thanks Gus, I will use those commands to build the logs. I assume I will
have to do a MAKE CLEAN before I try again right? I will try again later
tonight.

Post by Aragorn Inocencio
Hi, sorry about the mixup earlier. But I have recently tried installing
openmpi 3.0.0 using the instructions I found in the Reef3D manual (attached
below), so
./configure CC=gcc CXX=g++ F77=gfortran FC=gfortran
--prefix=/usr/local/openmpi
throws no errors, but again when I run the "make all" command next I am
1. #warning "fd_set and associated macros have been defined in sys/types
2. error: redefinition of struct hostent
3. A bunch of other errors similar to 2
4. A bunch of errors saying, "conflicting types for 'accept' bind,
connect etc.
5. "Expected declaration specifiers or '...' before '("
6. previous declaration of various functions
then all the way at the end it gives me an Error 1.
I'd like to apologize for my ignorance as I really have no background in
this area; I don't even know how to print all the errors to a txt file.

** If using sh/bash:

./configure CC=gcc CXX=g++ F77=gfortran FC=gfortran
--prefix=/usr/local/openmpi 2>&1 | tee my_configure.log

make 2>&1 | tee my_make.log

make install 2>&1 | tee my_make_install.log

** If using csh/tcsh:

./configure CC=gcc CXX=g++ F77=gfortran FC=gfortran
--prefix=/usr/local/openmpi |& tee my_configure.log

make |& tee my_make.log

make install |& tee my_make_install.log

I hope this helps,
Gus Correa

For what it's worth I have attached the config.log file.

Post by Aragorn Inocencio
​Inline image 1
_______________________________________________
users mailing list
https://lists.open-mpi.org/mailman/listinfo/users

[Aragorn Inocencio]

Good afternoon guys,

As instructed I have attached my log files for the configure, make, and
make install functions. Do you think there is hope for me getting this to
run in Windows via cygwin?

On Fri, Sep 22, 2017 at 5:30 AM, Aragorn Inocencio <

Post by Aragorn Inocencio
Good morning,
Thanks for the input Jeff; yes I am still doing this in Windows via
cygwin. I currently do not have a Linux machine.
Thanks Gus, I will use those commands to build the logs. I assume I will
have to do a MAKE CLEAN before I try again right? I will try again later
tonight.

Post by Aragorn Inocencio
Hi, sorry about the mixup earlier. But I have recently tried installing
openmpi 3.0.0 using the instructions I found in the Reef3D manual (attached
below), so
./configure CC=gcc CXX=g++ F77=gfortran FC=gfortran
--prefix=/usr/local/openmpi
throws no errors, but again when I run the "make all" command next I am
1. #warning "fd_set and associated macros have been defined in sys/types
2. error: redefinition of struct hostent
3. A bunch of other errors similar to 2
4. A bunch of errors saying, "conflicting types for 'accept' bind,
connect etc.
5. "Expected declaration specifiers or '...' before '("
6. previous declaration of various functions
then all the way at the end it gives me an Error 1.
I'd like to apologize for my ignorance as I really have no background in
this area; I don't even know how to print all the errors to a txt file.

./configure CC=gcc CXX=g++ F77=gfortran FC=gfortran
--prefix=/usr/local/openmpi 2>&1 | tee my_configure.log
make 2>&1 | tee my_make.log
make install 2>&1 | tee my_make_install.log
./configure CC=gcc CXX=g++ F77=gfortran FC=gfortran
--prefix=/usr/local/openmpi |& tee my_configure.log
make |& tee my_make.log
make install |& tee my_make_install.log
I hope this helps,
Gus Correa
For what it's worth I have attached the config.log file.

Post by Aragorn Inocencio
​Inline image 1
_______________________________________________
users mailing list
https://lists.open-mpi.org/mailman/listinfo/users

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

[Jeff Squyres (jsquyres)]

Check out this thread on the users archive:

https://www.mail-archive.com/***@lists.open-mpi.org/msg31602.html

including Marco's reply (Marco is the Cygwin Open MPI package maintainer).

Post by Aragorn Inocencio
Good afternoon guys,
As instructed I have attached my log files for the configure, make, and make install functions. Do you think there is hope for me getting this to run in Windows via cygwin?
Good morning,
Thanks for the input Jeff; yes I am still doing this in Windows via cygwin. I currently do not have a Linux machine.
Thanks Gus, I will use those commands to build the logs. I assume I will have to do a MAKE CLEAN before I try again right? I will try again later tonight.
Hi, sorry about the mixup earlier. But I have recently tried installing openmpi 3.0.0 using the instructions I found in the Reef3D manual (attached below), so
./configure CC=gcc CXX=g++ F77=gfortran FC=gfortran --prefix=/usr/local/openmpi
1. #warning "fd_set and associated macros have been defined in sys/types
2. error: redefinition of struct hostent
3. A bunch of other errors similar to 2
4. A bunch of errors saying, "conflicting types for 'accept' bind,
connect etc.
5. "Expected declaration specifiers or '...' before '("
6. previous declaration of various functions
then all the way at the end it gives me an Error 1.
I'd like to apologize for my ignorance as I really have no background in this area; I don't even know how to print all the errors to a txt file.
./configure CC=gcc CXX=g++ F77=gfortran FC=gfortran --prefix=/usr/local/openmpi 2>&1 | tee my_configure.log
make 2>&1 | tee my_make.log
make install 2>&1 | tee my_make_install.log
./configure CC=gcc CXX=g++ F77=gfortran FC=gfortran --prefix=/usr/local/openmpi |& tee my_configure.log
make |& tee my_make.log
make install |& tee my_make_install.log
I hope this helps,
Gus Correa
For what it's worth I have attached the config.log file.
​Inline image 1
_______________________________________________
users mailing list
https://lists.open-mpi.org/mailman/listinfo/users
_______________________________________________
users mailing list
https://lists.open-mpi.org/mailman/listinfo/users
--
Ismael Aragorn D. Inocencio
Civil Engineer
<logs.zip>_______________________________________________
users mailing list
https://lists.open-mpi.org/mailman/listinfo/users

--
Jeff Squyres
***@cisco.com

[Aragorn Inocencio]

Good morning Jeff,

Yes, I was also watching that thread for any developments as it's pretty
much the same scenario.

On Sep 27, 2017 11:49 PM, "Jeff Squyres (jsquyres)" <***@cisco.com>
wrote:

Check out this thread on the users archive:

https://www.mail-archive.com/***@lists.open-mpi.org/msg31602.html

including Marco's reply (Marco is the Cygwin Open MPI package maintainer).

On Sep 27, 2017, at 1:21 AM, Aragorn Inocencio <
Good afternoon guys,
As instructed I have attached my log files for the configure, make, and

make install functions. Do you think there is hope for me getting this to
run in Windows via cygwin?

On Fri, Sep 22, 2017 at 5:30 AM, Aragorn Inocencio <
Good morning,
Thanks for the input Jeff; yes I am still doing this in Windows via

cygwin. I currently do not have a Linux machine.

Thanks Gus, I will use those commands to build the logs. I assume I will

have to do a MAKE CLEAN before I try again right? I will try again later
tonight.

Hi, sorry about the mixup earlier. But I have recently tried installing

openmpi 3.0.0 using the instructions I found in the Reef3D manual (attached
below), so

./configure CC=gcc CXX=g++ F77=gfortran FC=gfortran

--prefix=/usr/local/openmpi

throws no errors, but again when I run the "make all" command next I am
1. #warning "fd_set and associated macros have been defined in sys/types
2. error: redefinition of struct hostent
3. A bunch of other errors similar to 2
4. A bunch of errors saying, "conflicting types for 'accept' bind,
connect etc.
5. "Expected declaration specifiers or '...' before '("
6. previous declaration of various functions
then all the way at the end it gives me an Error 1.
I'd like to apologize for my ignorance as I really have no background in

this area; I don't even know how to print all the errors to a txt file.

./configure CC=gcc CXX=g++ F77=gfortran FC=gfortran

--prefix=/usr/local/openmpi 2>&1 | tee my_configure.log

make 2>&1 | tee my_make.log
make install 2>&1 | tee my_make_install.log
./configure CC=gcc CXX=g++ F77=gfortran FC=gfortran

--prefix=/usr/local/openmpi |& tee my_configure.log

make |& tee my_make.log
make install |& tee my_make_install.log
I hope this helps,
Gus Correa
For what it's worth I have attached the config.log file.
​Inline image 1
_______________________________________________
users mailing list
https://lists.open-mpi.org/mailman/listinfo/users
_______________________________________________
users mailing list
https://lists.open-mpi.org/mailman/listinfo/users
--
Ismael Aragorn D. Inocencio
Civil Engineer
<logs.zip>_______________________________________________
users mailing list
https://lists.open-mpi.org/mailman/listinfo/users

--
Jeff Squyres
***@cisco.com