After reading the instruction manual for bgc, I ran this in the terminal:
/usr/local/src/bgcdist$ h5c++ -Wall -O2 -L/usr/include/gsl/lib -I/usr/local/gsl-1.15/include -o bgc
I got an error message:
The program 'h5c++' is currently not installed. You can install it by typing:
sudo apt-get install hdf5-helpers
So I did.
Note that I changed the directory for where to find GSL (highlighted) because I couldn't find it in usr/local. Eventually I gave up looking for it and uninstalled GSL, then downloaded it to install from source where I specified the directory using ./configure --prefix=/usr/local . (Spoiler alert: I mistyped this as "user/local" when I downloaded from source and this caused most of my problems later on. I believe I should have used the Ubuntu software center to resintall it and make sure I had all the GSL libraries I needed because when I reinstalled GSL at the very end, it worked fine from the software center.)
**********************************************************************
Done. The new package has been installed and saved to
/usr/local/src/gsl-1.16/gsl_1.16-1_amd64.deb
You can remove it from your system anytime using:
dpkg -r gsl
**********************************************************************
It still went into src. Hmm.
h5c++ -Wall -O2 -o bgc bgc_main.C bgc_func_readdata.C bgc_func_initialize.C bgc_func_mcmc.C bgc_func_write.C bgc_func_linkage.C bgc_func_ngs.C bgc_func_hdf5.C mvrandist.c -lgsl -lgslcblas
Be careful pasting from the manual, as in my terminal the underscores disappeared and then it couldn't find the files.
This gave me different errors, where it couldn't find GSL and compilation terminated.
h5c++ -Wall -O2 -L/usr/local/src/gsl-1.16 -I/usr/local/src/gsl-1.16 -o bgc bgc_main.C bgc_func_readdata.C bgc_func_initialize.C bgc_func_mcmc.C bgc_func_write.C bgc_func_linkage.C bgc_func_ngs.C bgc_func_hdf5.C mvrandist.c -lgsl -lgslcbla
This changed the missing files from those from gsl to one called hdf5.h.
h5c++ -Wall -O2 -L/usr/local/src/gsl-1.16 -I/usr/local/src/gsl-1.16 -prefix=/usr/local/src/hdf5-1.8.15-patch1/hdf5 -o bgc bgc_main.C bgc_func_readdata.C bgc_func_initialize.C bgc_func_mcmc.C bgc_func_write.C bgc_func_linkage.C bgc_func_ngs.C bgc_func_hdf5.C mvrandist.c -lgsl -lgslcbla
Nope.
Uninstalled hdf5. Then I found a recommendation to install an hdf5 cpp. Nope, still didn't work. (The observant or more experienced reader may note that I keep changing that last green-highlighted portion of the commands to have an s at the end or not. You will see below that this was of course a problem too.)
**********************************************************************
Finally, I was told that I had the prefixes wrongly specified (prefix just means it should be L or I, not actually saying prefix) and I had accidentally installed GSL into "user" instead of "usr" (the standard folder name). So this code below works because I needed to replace prefix with -I/, installed hdf5-dev and hdf5-serial-dev to get some of the files when they weren't found, and pointed the compiler to the wayward GSL files in the weird directory. I also sometimes forgot the s at the end of the green-highlighted command in previous attempts.
h5c++ -Wall -O2 -L/user/local/lib -L/usr/local/src/hdf5-1.8.15-patch1/hdf5/lib/ -I/usr/local/src/gsl-1.16 -I/usr/local/src/hdf5-1.8.15-patch1/hdf5/include/ -o bgc bgc_main.C bgc_func_readdata.C bgc_func_initialize.C bgc_func_mcmc.C bgc_func_write.C bgc_func_linkage.C bgc_func_ngs.C bgc_func_hdf5.C mvrandist.c -lgsl -lgslcblas
As with most things, essentially the installation process is following the error messages. If the compiler can't find a file, make sure the compile commands point to the correct directories (search for where the file is located), or go install the package/library or a related thing (like the -dev versions of hdf5) if it can't find it because it doesn't exist yet. Finally, when I went to run the compiled bgc, it turned out that the bgc program still couldn't find GSL in the misnamed "user" folder anyway. I uninstalled GSL (using the Ubuntu software center), reinstalled it, and bgc started then.
UPDATE 2016/07/14: This is much easier if you don't fill your commands with typos and install the required packages in the correct places. I upgraded to Ubuntu 16.04 LTS and it apparently removed GSL, so bgc no longer ran. I reinstalled gsl and the gsl development versions from the command line this time using 'sudo apt-get install gsl-bin libgsl-dev'. That presumably put them in the right place this time. I then navigated to the bgcdist folder where the files were stored, and ran the exact compiling command from the user manual/documentation. I was dreading a multi-hour fiasco again and it just worked. I think the moral of the story here is that this is a lot easier if you have installed packages a few times in Ubuntu by the time you attempt this, but it is doable even if you are brand new.
This changed the missing files from those from gsl to one called hdf5.h.
h5c++ -Wall -O2 -L/usr/local/src/gsl-1.16 -I/usr/local/src/gsl-1.16 -prefix=/usr/local/src/hdf5-1.8.15-patch1/hdf5 -o bgc bgc_main.C bgc_func_readdata.C bgc_func_initialize.C bgc_func_mcmc.C bgc_func_write.C bgc_func_linkage.C bgc_func_ngs.C bgc_func_hdf5.C mvrandist.c -lgsl -lgslcbla
Nope.
Uninstalled hdf5. Then I found a recommendation to install an hdf5 cpp. Nope, still didn't work. (The observant or more experienced reader may note that I keep changing that last green-highlighted portion of the commands to have an s at the end or not. You will see below that this was of course a problem too.)
**********************************************************************
Finally, I was told that I had the prefixes wrongly specified (prefix just means it should be L or I, not actually saying prefix) and I had accidentally installed GSL into "user" instead of "usr" (the standard folder name). So this code below works because I needed to replace prefix with -I/, installed hdf5-dev and hdf5-serial-dev to get some of the files when they weren't found, and pointed the compiler to the wayward GSL files in the weird directory. I also sometimes forgot the s at the end of the green-highlighted command in previous attempts.
h5c++ -Wall -O2 -L/user/local/lib -L/usr/local/src/hdf5-1.8.15-patch1/hdf5/lib/ -I/usr/local/src/gsl-1.16 -I/usr/local/src/hdf5-1.8.15-patch1/hdf5/include/ -o bgc bgc_main.C bgc_func_readdata.C bgc_func_initialize.C bgc_func_mcmc.C bgc_func_write.C bgc_func_linkage.C bgc_func_ngs.C bgc_func_hdf5.C mvrandist.c -lgsl -lgslcblas
As with most things, essentially the installation process is following the error messages. If the compiler can't find a file, make sure the compile commands point to the correct directories (search for where the file is located), or go install the package/library or a related thing (like the -dev versions of hdf5) if it can't find it because it doesn't exist yet. Finally, when I went to run the compiled bgc, it turned out that the bgc program still couldn't find GSL in the misnamed "user" folder anyway. I uninstalled GSL (using the Ubuntu software center), reinstalled it, and bgc started then.
UPDATE 2016/07/14: This is much easier if you don't fill your commands with typos and install the required packages in the correct places. I upgraded to Ubuntu 16.04 LTS and it apparently removed GSL, so bgc no longer ran. I reinstalled gsl and the gsl development versions from the command line this time using 'sudo apt-get install gsl-bin libgsl-dev'. That presumably put them in the right place this time. I then navigated to the bgcdist folder where the files were stored, and ran the exact compiling command from the user manual/documentation. I was dreading a multi-hour fiasco again and it just worked. I think the moral of the story here is that this is a lot easier if you have installed packages a few times in Ubuntu by the time you attempt this, but it is doable even if you are brand new.
