Installing migrate on a cluster

[Quinn Carvey]

Hello,

I'm trying to install migrate on a linux cluster and I am running into issues.

I downloaded the file (migrate-5.0.4.src.tar.gz) and uncompressed it (tar -xvf migrate-5.0.4.src.tar.gz). 

When I run ./configure from the src directory, my output is:

checking build system type... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
checking target system type... x86_64-pc-linux-gnu
checking for gmake... gmake
checking for clang... no
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... 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... -std=gnu11
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 -std=gnu11
C++-compiler:g++
CFLAGS: -I/home/scarvey/miniconda3/envs/stacks_venv/include/gsl -I/home/scarvey/miniconda3/envs/stacks_venv/include/gsl
=======================================================================
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... yes
checking for gzbuffer... 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: linux-gnu  Linux  linux-gnu
System CPU: x86_64
-----------------------------------------------------------------------
 
 MIGRATE-N is now setup

When I run 'make' the output, I get several errors (output attached in a text file). I tried the installation options discussed in another post (https://groups.google.com/g/migrate-support/c/DhrW5LQGfGI/m/PYH9113i27wJ), but unfortunately those options did not work for me. 

I'm waiting for the system administrator to configure openmpi and so I am trying to install the non-parallel version of migrate to run through the examples and tutorials.

I would appreciate any help you can provide to get migrate running on my system. Thank you!

Quinn

[Peter Beerli]

Open the Makefile

and search for 

STDCPLUS          =     

and replace with

STDCPLUS          = -lstdc++    

it looks like your gcc is not finding the c++ bindings

peter

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<migrate_make_output_error.rtf>

[Quinn Carvey]

That seems to have worked, I'm successfully running one of the example datasets. Thank you so much! Hopefully I'll hear back from the system administrator about setting up the parallel version soon. Will I want to keep the change to the Makefile when configuring the parallel migrate version?

Quinn

[Peter Beerli]

yes you want to keep that flag

the Makefile will work for parallel migrate but you should do

make clean

make mpis

to make sure thatyou do not get non-parallel version, on somes systems some users were able to compile in a weird way with fragments of single cpu code.

Peter

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[Quinn Carvey]

Hi Peter,

I think I may have successfully installed openmpi in a virtual environment that I can access on the remote server. When I type 'mpicc --version' I get: "x86_64-conda-linux-gnu-cc (Anaconda gcc) 11.2.0", which I think is a good sign. I ran 'make clean' then 'make mpis', but I am getting further errors (attached).

I appreciate any guidance you can offer.

Quinn

[Peter Beerli]

I never had any success with compiling using the anaconda-derived compiler chain, in particular with openmpi, but your problem seems to be that the linker is not finding the correct libraries, it does not find memcpy which is surely a standard function in any C library, so I guess it is a mismatch in version of compiler and linker.

Peter

To view this discussion on the web visit https://groups.google.com/d/msgid/migrate-support/62c5b503-9847-4201-a949-9ba234cfae84n%40googlegroups.com.
<makempis_output.rtf><makeclean_output.rtf>