Haskell stack not seeing libgmp.so.10 provided in an environment module - environment-variables

Question

I'm starting to try to work on a Linux computing cluster where some programs and libraries are made available through a system of environment modules.
I would like to install Haskell programs using stack (I should probably say that I'm not yet very familiar with stack).
stack is available as a module, so after doing module load stack, I tried stack setup, which failed, complaining about gmp missing:
$ stack setup
Preparing to install GHC (gmp4) to an isolated location.
This will not interfere with any system-level installation.
Downloaded ghc-gmp4-8.0.1.
Installed GHC.
The GHC located at
/pasteur/homes/bli/.stack/programs/x86_64-linux/ghc-gmp4-8.0.1/bin/ghc
failed to compile a sanity check. Please see:
http://docs.haskellstack.org/en/stable/install_and_upgrade/
for more information. Exception was:
Running
/pasteur/homes/bli/.stack/programs/x86_64-linux/ghc-gmp4-8.0.1/bin/ghc
/tmp/stack-sanity-check24665/Main.hs -no-user-package-db in directory
/tmp/stack-sanity-check24665/ exited with ExitFailure 1
[1 of 1] Compiling Main (
/tmp/stack-sanity-check24665/Main.hs, /tmp/stack-sanity-check24665/Main.o )
Linking /tmp/stack-sanity-check24665/Main ...
/usr/bin/ld: cannot find -lgmp
collect2: ld returned 1 exit status
`gcc' failed in phase `Linker'. (Exit code: 1)
The admin of the cluster told me that gmp was also available as an environment module, so I did module load gmp before trying again, and it seemed to work:
$ stack setup
Writing implicit global project config file to:
/pasteur/homes/bli/.stack/global-project/stack.yaml
Note: You can change the snapshot via the resolver field there.
Using latest snapshot resolver: lts-8.23
Downloaded lts-8.23 build plan.
Selected mirror https://s3.amazonaws.com/hackage.fpcomplete.com/
Downloading root
Selected mirror https://s3.amazonaws.com/hackage.fpcomplete.com/
Downloading timestamp
Downloading snapshot
Downloading mirrors
Cannot update index (no local copy)
Downloading index
Updated package list downloaded
Populated index cache.
Preparing to install GHC (gmp4) to an isolated location.
This will not interfere with any system-level installation.
Downloaded ghc-gmp4-8.0.2.
Installed GHC.
stack will use a sandboxed GHC it installed
For more information on paths, see 'stack path' and 'stack exec env'
To use this GHC and packages outside of a project, consider using:
stack ghc, stack ghci, stack runghc, or stack exec
Then I tried to install hlint using stack:
$ stack install hlint
clock-0.7.2: configure
uniplate-1.6.12: download
clock-0.7.2: build
old-time-1.1.0.3: configure
Package old-time uses a custom Cabal build, but does not use a
custom-setup stanza
Not using the explicit setup deps approach based on configuration
Strongly recommend fixing the package's cabal file
old-time-1.1.0.3: build
Package old-time uses a custom Cabal build, but does not use a
custom-setup stanza
uniplate-1.6.12: configure
Not using the explicit setup deps approach based on configuration
Strongly recommend fixing the package's cabal file
uniplate-1.6.12: build
uniplate-1.6.12: copy/register
Progress: 3/7
-- While building package old-time-1.1.0.3 using:
/tmp/stack8279/old-time-1.1.0.3/.stack-work/dist/x86_64-linux-gmp4/Cabal-1.24.2.0/setup/setup
--builddir=.stack-work/dist/x86_64-linux-gmp4/Cabal-1.24.2.0 build
--ghc-options " -ddump-hi -ddump-to-file"
Process exited with code: ExitFailure 1
Logs have been written to:
/pasteur/homes/bli/.stack/global-project/.stack-work/logs/old-time-1.1.0.3.log
[1 of 2] Compiling Main (
/tmp/stack8279/old-time-1.1.0.3/Setup.hs,
/tmp/stack8279/old-time-1.1.0.3/.stack-work/dist/x86_64-linux-gmp4/Cabal-1.24.2.0/setup/Main.o
)
[2 of 2] Compiling StackSetupShim (
/pasteur/homes/bli/.stack/setup-exe-src/setup-shim-mPHDZzAJ.hs,
/tmp/stack8279/old-time-1.1.0.3/.stack-work/dist/x86_64-linux-gmp4/Cabal-1.24.2.0/setup/StackSetupShim.o
)
Linking
/tmp/stack8279/old-time-1.1.0.3/.stack-work/dist/x86_64-linux-gmp4/Cabal-1.24.2.0/setup/setup
...
Configuring old-time-1.1.0.3...
configure: WARNING: unrecognized options: --with-compiler
checking for gcc... /usr/bin/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 we are using the GNU C compiler... yes
checking whether /usr/bin/gcc accepts -g... yes
checking for /usr/bin/gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... /usr/bin/gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking sys/time.h usability... yes
checking sys/time.h presence... yes
checking for sys/time.h... yes
checking sys/timeb.h usability... yes
checking sys/timeb.h presence... yes
checking for sys/timeb.h... yes
checking time.h usability... yes
checking time.h presence... yes
checking for time.h... yes
checking for ftime... yes
checking for gmtime_r... yes
checking for localtime_r... yes
checking for gettimeofday... yes
checking whether struct tm is in sys/time.h or time.h... time.h
checking for struct tm.tm_zone... yes
checking whether time.h and sys/time.h may both be included... yes
checking for sys/time.h... (cached) yes
checking whether altzone is declared... no
configure: creating ./config.status
config.status: creating include/HsTimeConfig.h
configure: WARNING: unrecognized options: --with-compiler
Building old-time-1.1.0.3...
Preprocessing library old-time-1.1.0.3...
.stack-work/dist/x86_64-linux-gmp4/Cabal-1.24.2.0/build/System/Time_hsc_make:
error while loading shared libraries: libgmp.so.10: cannot open shared
object file: No such file or directory
running
.stack-work/dist/x86_64-linux-gmp4/Cabal-1.24.2.0/build/System/Time_hsc_make
failed (exit code 127)
command was:
.stack-work/dist/x86_64-linux-gmp4/Cabal-1.24.2.0/build/System/Time_hsc_make
>.stack-work/dist/x86_64-linux-gmp4/Cabal-1.24.2.0/build/System/Time.hs
-- While building package clock-0.7.2 using:
/pasteur/homes/bli/.stack/setup-exe-cache/x86_64-linux-gmp4/Cabal-simple_mPHDZzAJ_1.24.2.0_ghc-8.0.2
--builddir=.stack-work/dist/x86_64-linux-gmp4/Cabal-1.24.2.0 build
--ghc-options " -ddump-hi -ddump-to-file"
Process exited with code: ExitFailure 1
Logs have been written to:
/pasteur/homes/bli/.stack/global-project/.stack-work/logs/clock-0.7.2.log
Configuring clock-0.7.2...
Building clock-0.7.2...
Preprocessing library clock-0.7.2...
Clock.hsc:44:1: warning: "hsc_alignment" redefined
In file included from
.stack-work/dist/x86_64-linux-gmp4/Cabal-1.24.2.0/build/System/Clock_hsc_make.c:1:
/pasteur/homes/bli/.stack/programs/x86_64-linux/ghc-gmp4-8.0.2/lib/ghc-8.0.2/template-hsc.h:88:1:
warning: this is the location of the previous definition
.stack-work/dist/x86_64-linux-gmp4/Cabal-1.24.2.0/build/System/Clock_hsc_make:
error while loading shared libraries: libgmp.so.10: cannot open shared
object file: No such file or directory
running
.stack-work/dist/x86_64-linux-gmp4/Cabal-1.24.2.0/build/System/Clock_hsc_make
failed (exit code 127)
command was:
.stack-work/dist/x86_64-linux-gmp4/Cabal-1.24.2.0/build/System/Clock_hsc_make
>.stack-work/dist/x86_64-linux-gmp4/Cabal-1.24.2.0/build/System/Clock.hs
It seems that when compiling ghc, stack was able to see gmp, but not when installing some packages.
I notice this warning: configure: WARNING: unrecognized options: --with-compiler. I don't know if this is relevant.
The environment module system seems to work by exporting some environment variables:
$ module show gmp
-------------------------------------------------------------------
/local/gensoft2/devmodules/gmp/6.0.0:
module-whatis Set environnement for gmp (6.0.0)
module-whatis topic_3316
prepend-path LIBRARY_PATH /local/gensoft2/lib/gmp/6.0.0/lib
prepend-path LD_RUN_PATH /local/gensoft2/lib/gmp/6.0.0/lib
prepend-path -d LDFLAGS -L/local/gensoft2/lib/gmp/6.0.0/lib
prepend-path CMAKE_LIBRARY_PATH /local/gensoft2/lib/gmp/6.0.0/lib
prepend-path C_INCLUDE_PATH /local/gensoft2/lib/gmp/6.0.0/include
prepend-path CPLUS_INCLUDE_PATH /local/gensoft2/lib/gmp/6.0.0/include
prepend-path CMAKE_INCLUDE_PATH /local/gensoft2/lib/gmp/6.0.0/include
prepend-path -d CPPFLAGS -I/local/gensoft2/lib/gmp/6.0.0/include
setenv GMP_ROOT /local/gensoft2/lib/gmp/6.0.0
-------------------------------------------------------------------
The administrator told me that these environment variable are not always taken into account, and suggested to export LDFLAGS="-Wl,-rpath,$GMP_ROOT/lib $LDFLAGS" in my environment before trying, but this did not seem to have any effect on the issue.
I still obtain the following: error while loading shared libraries: libgmp.so.10: cannot open shared object file: No such file or directory
How can I get stack to reliably take into account development libraries that the environment modules system provides?
Edit
It seems that I can give the missing library paths on the command line to stack as follows:
$ stack --extra-lib-dirs=/local/gensoft2/lib/gmp/6.0.0/lib --extra-include-dirs=/local/gensoft2/lib/gmp/6.0.0/include install hlint
old-time-1.1.0.3: configure
Package old-time uses a custom Cabal build, but does not use a custom-setup stanza
Not using the explicit setup deps approach based on configuration
Strongly recommend fixing the package's cabal file
old-time-1.1.0.3: build
Package old-time uses a custom Cabal build, but does not use a custom-setup stanza
Not using the explicit setup deps approach based on configuration
Strongly recommend fixing the package's cabal file
clock-0.7.2: configure
clock-0.7.2: build
clock-0.7.2: copy/register
extra-1.5.3: download
extra-1.5.3: configure
extra-1.5.3: build
old-time-1.1.0.3: copy/register
Package old-time uses a custom Cabal build, but does not use a custom-setup stanza
Not using the explicit setup deps approach based on configuration
Strongly recommend fixing the package's cabal file
Package old-time uses a custom Cabal build, but does not use a custom-setup stanza
Not using the explicit setup deps approach based on configuration
Strongly recommend fixing the package's cabal file
cpphs-1.20.8: download
cpphs-1.20.8: configure
cpphs-1.20.8: build
extra-1.5.3: copy/register
cpphs-1.20.8: copy/register
haskell-src-exts-1.18.2: download
haskell-src-exts-1.18.2: configure
haskell-src-exts-1.18.2: build
haskell-src-exts-1.18.2: copy/register
hlint-1.9.41: download
hlint-1.9.41: configure
hlint-1.9.41: build
hlint-1.9.41: copy/register
Completed 6 action(s).
Copying from /pasteur/homes/bli/.stack/snapshots/x86_64-linux-gmp4/lts-8.23/8.0.2/bin/hlint to /pasteur/homes/bli/.local/bin/hlint
Copied executables to /pasteur/homes/bli/.local/bin:
- hlint
Is there a way to have this done automatically for every possible development library loaded by module?

Answer 1

I'm not sure this is completely reliable (environment modules for development libraries might not all export these variables), but passing -extra-include-dirs=${CMAKE_INCLUDE_PATH} and --extra-lib-dirs=${CMAKE_LIBRARY_PATH} to stack seems to work at least when installing hlint, scan and doctest.
I'm a bit confused about what would be the correct configuration file to use, and how, to make this automatic.
It seems that the corresponding settings in ~/.stack/config.yaml are taken into account (although the documentation mentions ~/.stack/global-project/stack.yaml).
The above-mentioned environment variables cannot be used as-is in the config file. I haven't determined what the exact reason. This could be either because their expansion results in something not syntactically correct (paths separated by ":" instead of ","), or because only plain text is permitted in the config file.
Therefore, the following works in the present case, but is not a general solution:
extra-include-dirs: [/local/gensoft2/lib/gmp/6.0.0/include]
extra-lib-dirs: [/local/gensoft2/lib/gmp/6.0.0/lib]