gfortran compile error

dulap · 01-17-2020, 10:28 AM

I'm new to linux and I tried to compile OTIS (OSU Tidal Inversion Software) on Ubuntu. I got following error. How could I solve this?

deallocate(zeq0%z,zeq0%mz,zeq0%cid%idc,zeq0%cid%cons,&
1
zeq0%cid%group,zeq0%cid,zeq0,P)
2
Error: Allocate-object at (1) is subobject of object at (2)
ZEQset_NPG.f90:123:24:

deallocate(zeq0%z,zeq0%mz,zeq0%cid%idc,zeq0%cid%cons,&
1
zeq0%cid%group,zeq0%cid,zeq0,P)
2

Thanks

business_kid · 01-18-2020, 12:36 PM

Welcome to LQ, dulap.

Fortran? That's a weird one. Are you sure the compiler is installed? To check, run

Code:

ls /usr/bin/gcc*

and look for gcc-fortran unless you're using some other compiler. Have you a link to that software?

Your output makes no sense to me. It looks more like a crash, or a rubbish in --> rubbish out scenario.
Next the package: you did follow the instructions for compiling? (usually ./configure {lots of options}; make; sudo make install). If they're using cmake or any other build system, let us know

Run 'make clean', and follow the instructions. If it pukes again, in the terminal, hit up-arrow and return, and post the entire output.

rnturn · 01-18-2020, 03:47 PM

Quote:

Originally Posted by dulap

I'm new to linux and I tried to compile OTIS (OSU Tidal Inversion Software) on Ubuntu. I got following error. How could I solve this?

deallocate(zeq0%z,zeq0%mz,zeq0%cid%idc,zeq0%cid%cons,&
1
zeq0%cid%group,zeq0%cid,zeq0,P)
2
Error: Allocate-object at (1) is subobject of object at (2)
ZEQset_NPG.f90:123:24:

deallocate(zeq0%z,zeq0%mz,zeq0%cid%idc,zeq0%cid%cons,&
1
zeq0%cid%group,zeq0%cid,zeq0,P)
2

Thanks

I haven't used the Fortran allocate/deallocate statements before but from I have read about it, it seems to be a way of doing dynamic memory allocation (similar to malloc/free in C). My guess is that what is being deallocated would break some other allocated bit of memory that depends on it.

I may be wrong (and often am; just ask the missus) but my guess is that this is a little too "niche" for a helpful response from LQ users. My gut tells me that without knowing the internals of what you're trying to compile you're probably going to have to find a user group that knows about this software package in detail and pick their collective brains. I was thinking of downloading the source tar archive but, frankly, I'm balking at downloading 664MB of compressed sources from the site in hopes of finding a 'README.1st' file to look for clues to your problem. (I'm a bit surprised someone is still using 'compress'; kind of old-school.) There are email addresses on the project site at Oregon State---you might consider shooting a note to one of them an email asking for a name/email address of someone you can contact with questions about compiling the sources.

Good luck...

knudfl · 01-19-2020, 06:35 AM

@dulap : Please specify Ubuntu version.

The OTIS program has time stamps `2013´. You may need an older compiler.

My test :

Code:

$ cd OTISoo/bin  
      ## edit 'makefile' line 23 to gfortran45 (version gcc-4.5.4)
$ make linux.all         ## the terminal output is attached

Result :

Code:

OTISoo/bin/
├── bhat_samp
├── data_cooker
├── Diffuse
├── Fwd_fac
├── Lat_lon
├── Makedat
├── mkB
├── mkFrv
├── mk_g_ll
├── mk_grid
├── ob_eval
├── reduce_B
├── repX
├── rlcX
├── rpx_to_rp
├── Scfac
├── Sml_df
├── stats_rlz
├── Sumreps
└── Varest

Using gfortran version 9.2.0 fails.
The error output is very different from your errors.
Reason :
Might be caused by the special Debian patching used by Ubuntu (the 100? gcc patches.)
I.e. an original gcc/g++/gfortran happens to work better with old programs.
-

knudfl · 01-20-2020, 11:04 AM

OTIS fails with the default gfortran in Ubuntu 12.04, 14.04, 16.04, 18.04 .
OTIS compiles the 20 executable with gfortran-4.4 in the tested Ubuntu versions :
Edit `makefile´ line 23 to gfortran-4.4

`gfortran-4.4´ is not available for e.g. Ubuntu 18.04 : Install from file →
4 packages: gfortran-4.4_4.4.7-8ubuntu.tar
https://drive.google.com/file/d/1WCK...ew?usp=sharing

Download, unpack .... and install :

Code:

sudo apt install libgfortran3
sudo dpkg -i cpp-4.4_4.4.7-8ubuntu1_amd64.deb gcc-4.4_4.4.7-8ubuntu1_amd64.deb gcc-4.4-base_4.4.7-8ubuntu1_amd64.deb gfortran-4.4_4.4.7-8ubuntu1_amd64.deb

dulap · 01-20-2020, 04:06 PM

@knudfl: I successfully compiled OTIS thanks to your great help. Thank a lot for spending your valuable time with this problem.

dulap · 01-20-2020, 04:09 PM

@business_kid: Thanks for your reply. I succeeded instruction given by knudfl

dulap · 01-20-2020, 04:12 PM

@rnturn: Thanks for your instructions. I solved problem using the posts from knudfl