binary not created

[aryahi anil kumar]

Hi, 

I am trying to run migrate on a cygwin virtual machine with open mpi. 

However, make mpis or make is not creating the migrate-n-mpi file or the migrate-n file. 

I am not sure what I should do to create the binary. I have already checked for the STDCPLUS as described in this thread. 

This is the log 

$ ./configure
make checking build system type... instx86_64-pc-cygwin
checking host system type... x86_64-pc-cygwin
checking target system type... x86_64-pc-cygwin
alchecking for gmake... make
checking for clang... no
checking for gcc... gcc
lchecking whether the C compiler works... yes
checking for C compiler default output file name... a.exe
checking for suffix of executables... .exe
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether the compiler supports GNU C... yes
checking whether gcc accepts -g... yes
checking for gcc option to enable C11 features... none needed
checking for clang... no
checking for g++... g++
checking whether the compiler supports GNU C++... yes
checking whether g++ accepts -g... yes
checking for g++ option to enable C++11 features... none needed
C-compiler:  gcc
C++-compiler:g++
CFLAGS: -O3  -funroll-loops -fomit-frame-pointer  -falign-loops=16  -Dx86_64
=======================================================================
checking for a BSD-compatible install... /usr/bin/install -c
checking for pthread_create in -lpthread... yes
checking for MPI_Init in -lmpi... yes
checking for exp in -lm... yes
checking for stdio.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for strings.h... yes
checking for sys/stat.h... yes
checking for sys/types.h... yes
checking for unistd.h... yes
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for limits.h... yes
checking for strings.h... (cached) yes
checking for pthread.h... yes
checking for an ANSI C-conforming const... yes
checking for size_t... yes
checking for int... yes
checking whether struct tm is in sys/time.h or time.h... time.h
checking for inline... inline
checking for strftime... yes
checking for strcspn... yes
checking for strsep... yes
checking for strdup... yes
checking for lgamma... yes
checking which zlib implementation to use... autodetect
checking for main in -lz... no
./configure: line 4995: =no: command not found
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/conf.h
config.status: src/conf.h is unchanged
=======================================================================
Migrate subversion: May-09-2022
Hardware: pc
System OS: cygwin  CYGWIN_NT-10.0-22621  cygwin
System CPU: x86_64
-----------------------------------------------------------------------

 MIGRATE-N is now setup
 to compile the program you need to type one of the
 commands below (ordered by preference):

 SINGLE CPU machines
     make        # with PDF output support
                 # this might fail on first attempt,
                 # if the make fails, please let me know
                 # often linking fails because the C++ pdf library
                 # and the core migrate parts (C) mismatch
                 # check the Makefile line for STDLIB= -lstdc++

 SMP machines  more than 1 CPU in machine
     make thread # try this but I have not tested in a while needs pthreads
     make        # on macs running MacOS using GrandCentral

 PARALLEL Computers, Clusters with MPI software such as openmpi or mpich2
     make clean       # to make sure that no single-CPU object is available
     make mpis        # each cpu-core can be treated as a node

After this point the program automatically takes me back to the cygwin terminal where I cannot enter the next make command. <pic attached>

I would really appreciate any help to get the migrate-n-mpi binary running. 

I have used migrate on Windows but it has been running for a day now. I wanted to use all 4 of my CPU cores to speed up the process, I am running openmpi on my laptop and not a computer cluster.

Thanks in advance.

Arya

[Peter Beerli]

your cygwin is missing the make, check your installation of cygwin and add make, this is not an issue with migrate 

[I cannot help with cygwin]

Peter

<Screenshot 2023-05-03 144954.png>

I would really appreciate any help to get the migrate-n-mpi binary running. 

I have used migrate on Windows but it has been running for a day now. I wanted to use all 4 of my CPU cores to speed up the process, I am running openmpi on my laptop and not a computer cluster.

Thanks in advance.

Arya

--
You received this message because you are subscribed to the Google Groups "migrate-support" group.
To unsubscribe from this group and stop receiving emails from it, send an email to migrate-suppo...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/migrate-support/69a2f1de-1589-491f-b19d-cbb34f219e5cn%40googlegroups.com.
<Screenshot 2023-05-03 144954.png>

[aryahi anil kumar]

Dear Peter, 

Thank you so much for the prompt response. 

I was able to resolve the issue by installing the make package.

However, my migrate-n-mpi results in a segmentation fault. 

I tried running a hello-world code and it runs giving me the results as expected. 

Hello world!  I am process number: 0 on processor machinename
Hello world!  I am process number: 1 on processor  machinename
Hello world!  I am process number: 2 on processor  machinename
Hello world!  I am process number: 3 on processor machinename

I would be very thankful if you could have a look, I am not sure if the problem is with openmpi or cygwin.

I have reinstalled openmpi. I am struggling to identify what exactly is causing the error as my hello-world file seems to work.

$ mpirun  -np 4 --hostfile myhosts.hosts migrate-n-mpi parmfile
[machinename:01130] PMIX ERROR: INIT in file /pub/devel/openmpi/v4.0/openmpi-4.1.5-1.x86_64/src/openmpi-4.1.5/opal/mca/pmix/pmix3x/pmix/src/mca/gds/ds21/gds_ds21_lock_pthread.c at line 187
[ machinename  :01130] PMIX ERROR: SUCCESS in file /pub/devel/openmpi/v4.0/openmpi-4.1.5-1.x86_64/src/openmpi-4.1.5/opal/mca/pmix/pmix3x/pmix/src/mca/common/dstore/dstore_base.c at line 2454
[ machinename  :01130] PMIX ERROR: INIT in file /pub/devel/openmpi/v4.0/openmpi-4.1.5-1.x86_64/src/openmpi-4.1.5/opal/mca/pmix/pmix3x/pmix/src/mca/gds/ds12/gds_ds12_lock_pthread.c at line 138
[ machinename  :01130] PMIX ERROR: SUCCESS in file /pub/devel/openmpi/v4.0/openmpi-4.1.5-1.x86_64/src/openmpi-4.1.5/opal/mca/pmix/pmix3x/pmix/src/mca/common/dstore/dstore_base.c at line 2454
[ machinename  :01131] PMIX ERROR: ERROR in file /pub/devel/openmpi/v4.0/openmpi-4.1.5-1.x86_64/src/openmpi-4.1.5/opal/mca/pmix/pmix3x/pmix/src/mca/gds/ds12/gds_ds12_lock_pthread.c at line 168
[DESKTOP-7M321R2:01132] PMIX ERROR: ERROR in file /pub/devel/openmpi/v4.0/openmpi-4.1.5-1.x86_64/src/openmpi-4.1.5/opal/mca/pmix/pmix3x/pmix/src/mca/gds/ds12/gds_ds12_lock_pthread.c at line 168
[ machinename  :01133] PMIX ERROR: ERROR in file /pub/devel/openmpi/v4.0/openmpi-4.1.5-1.x86_64/src/openmpi-4.1.5/opal/mca/pmix/pmix3x/pmix/src/mca/gds/ds12/gds_ds12_lock_pthread.c at line 168
[ machinename  :01134] PMIX ERROR: ERROR in file /pub/devel/openmpi/v4.0/openmpi-4.1.5-1.x86_64/src/openmpi-4.1.5/opal/mca/pmix/pmix3x/pmix/src/mca/gds/ds12/gds_ds12_lock_pthread.c at line 168
before option master
--------------------------------------------------------------------------
Sorry!  You were supposed to get help about:
    normal-termination-but
from the file:
    help-errmgr-base.txt
But I couldn't find that topic in the file.  Sorry!
--------------------------------------------------------------------------
--------------------------------------------------------------------------
mpirun noticed that process rank 0 with PID 0 on node  machinename  exited on signal 11 (Segmentation fault).
--------------------------------------------------------------------------

Once again, I am very grateful for your help. 

Cheers,

Arya