Could not find CFITSIO

[tjgarci2]

Hi! I was trying to install SYNAPPS and SYN++ but I seem to have run into a problem. I have CFITSIO properly installed but it doesn't seem like when I run ./configure for es-0.98.1 it can't find it. Attached is a screenshot.

[rcthomas]

Hi, can you tell me what arguments (if any) you gave to configure when you ran it, and what the include and library path to CFITSIO looks like on your machine?

Is this a machine with a lot (hundreds) of cores? If not you might want to skip the SYNAPPS build.

[tskisner]

Could you attach the generated "config.log" file to this issue?

On 12/09/2015 08:15 PM, tjgarci2 wrote:

Hi! I was trying to install SYNAPPS and SYN++ but I seem to have run
into a problem. I have CFITSIO properly installed but it doesn't seem
like when I run ./configure for es-0.98.1 it can't find it. Attached is
a screenshot.
screenshot from 2015-12-09 22-12-26
https://cloud.githubusercontent.com/assets/16234842/11706842/4a17e200-9ec2-11e5-88ed-325f1b86b421.png

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Reply to this email directly or view it on GitHub
#9.

[tjgarci2]

config.docx

I ran it with ./configure --with-cfitsio-include=/Astro/cfitsio/include --with-cfitsio-lib=/Astro/cfitsio/lib
And the paths should be ~/Astro/cfitsio/include and ~/Astro/cfitsio/lib
I'm also just on an Intel i7 laptop running Ubuntu so I should probably skip the SYNAPPS build.

[tskisner]

Try specifying the full paths (no ~) to your home directory in that command.

If that still does not work, then as a workaround, can you try configuring like this:
%> CPPFLAGS=-I/home//Astro/cfitsio/include LDFLAGS=-L/home//Astro/cfitsio/lib ./configure (... then same options as before)

Here I assume that your cfitsio install location has been put into your LD_LIBRARY_PATH, etc.

[tjgarci2]

Where would I go to put my install location into LD_LIBRARY_PATH and would there be anything else I should edit that I might be missing?

[tskisner]

Is there some particular reason you are installing dependencies manually, rather than doing:

%> sudo apt-get install libcfitsio-dev

? There are certainly reasons for compiling things yourself. But doing so usually requires configuring your shell environment. Specifically you should append to PATH any locations containing executable software, you should append to CPATH any include directories, and you should append to LIBRARY_PATH and LD_LIBRARY_PATH and directories containing libraries. How you modify those variables depends on which shell you are using.

[tjgarci2]

I didn't realize I could install CFITSIO through apt-get so...
I ran ES ./configure && make && make install. These are the results. The first screenshot is ./configure and the second is make and make install respectively.

[tskisner]

It looks like your compiler environment is not standard- I see that libstdc++ is coming from "/home/tjsgarcia/mesasdk". Do you have the standard ubuntu development tools installed?

%> apt-get install build-essential

What c++ compiler are you using?:

%> which g++
%> g++ --version

It is critical that your g++ version is used with a compatible libstdc++. It looks like from your error that the system-installed g++ is trying to use incompatible C++ standard headers/library.

[tjgarci2]

I have the standard ubuntu development tools. I don't know why it's finding mesasdk's g++. Is there a way to have it find the standard g++ and not mesasdk's?

[tjgarci2]

Also when I run
%> which g++
%> g++ --version
I get

tjsgarcia@tgarcia-K55VD:$ which g++
/home/tjsgarcia/mesasdk/bin/g++
tjsgarcia@tgarcia-K55VD:$ g++ --version
g++.exec (GCC) 4.9.4 20150827 (prerelease)
Copyright (C) 2015 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

tjsgarcia@tgarcia-K55VD:~$

[rcthomas]

MESA must have some way of deactivating its SDK toolchain for things like this that you can use. Have you checked the documentation about getting their toolchain backed out of your paths etc? They probably had you add some lines of code to your shell resource file when you installed (or their installer did it for you). These would be things that set PATH and LD_LIBRARY_PATH and so on.

[tjgarci2]

For now I do not need MESASDK so I deleted it and ran configure, make, and make install again. I think configure and make have worked but I'm unsure about make install.

[rcthomas]

Please see https://c3.lbl.gov/es/#installation, in particular the part about --prefix. If you have super-user privileges on this machine you should be able to skip specifying prefix and do "sudo make install" and it will put SYN++ etc under /usr/local. Otherwise, if you do not have super-user privileges on this machine you will want to specify a --prefix value as mentioned in the docs.

[tjgarci2]

The part of the website where it says "when all is said and done" I have the structure underneath except I didn't install synapps. So I think I've installed it correctly. Thank you for your time.

[rcthomas]

Great!