Installing FFTW2 manually and including it in spack/lmod¶
Installing FFTW 2¶
A fix has been published on github, but for some reason not yet
merged into the master.
Anyhow, look at the file package.py in $SPACK_ROOT/var/spack/repos/builtin/packages/fftw/package.py and use this one instead.
Or have a look at this.
The notes below this line are deprecated, but should still work.
For some reason, spack fails to install FFTW 2. On my machine, I get this error:
$ spack install fftw@2.1.5
==> libsigsegv is already installed in /home/mivkov/applications/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.3.0/libsigsegv-2.11-oromhtnsg3whjgy4ufgufwwwxe3iadp7
==> m4 is already installed in /home/mivkov/applications/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.3.0/m4-1.4.18-vypfbpxo4do2ieh3hf7fbxpyz66b5zav
==> perl@5.26.1 : externally installed in /usr
==> perl@5.26.1 : already registered in DB
==> autoconf is already installed in /home/mivkov/applications/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.3.0/autoconf-2.69-k35byc24q67run3egd2orhoaj54nmzb7
==> automake is already installed in /home/mivkov/applications/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.3.0/automake-1.16.1-a2a6vcqlt6ayxo5wdmt4f4ksajhn4ihj
==> libtool is already installed in /home/mivkov/applications/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.3.0/libtool-2.4.6-jher54m7efbgqjarpywxcb3yxmelyswk
==> texinfo is already installed in /home/mivkov/applications/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.3.0/texinfo-6.5-hupxyymn5eiwtzg42j7phsl574nys3kl
==> findutils is already installed in /home/mivkov/applications/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.3.0/findutils-4.6.0-capl6zymtrqxltqnfqiykagcciyumy6z
==> mpich is already installed in /home/mivkov/applications/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.3.0/mpich-3.2.1-goluh6hkr5xlspftwizqxlysbdtghk67
==> Installing fftw
==> Using cached archive: /home/mivkov/applications/spack/var/spack/cache/fftw/fftw-2.1.5.tar.gz
==> Staging archive: /home/mivkov/applications/spack/var/spack/stage/fftw-2.1.5-wkxg7i7u6rsmzvtllkzob2ge5dx5q4lq/fftw-2.1.5.tar.gz
==> Created stage in /home/mivkov/applications/spack/var/spack/stage/fftw-2.1.5-wkxg7i7u6rsmzvtllkzob2ge5dx5q4lq
==> No patches needed for fftw
==> Building fftw [AutotoolsPackage]
==> Executing phase: 'autoreconf'
==> Executing phase: 'configure'
==> Executing phase: 'build'
==> Error: ProcessError: Command exited with status 2:
'make' '-j8'
4 errors found in build log:
1623 /bin/bash ../libtool --mode=link /home/mivkov/applications/spack/lib/spack
/env/gcc/gcc -O3 -fomit-frame-pointer -fno-schedule-insns -fschedule-insn
s2 -malign-double -fstrict-aliasing -pthread -o fftw_test fftw_test.o t
est_main.o ../fftw/libdfftw.la -lm
1624 mkdir .libs
1625 /home/mivkov/applications/spack/lib/spack/env/gcc/gcc -O3 -fomit-frame-poi
nter -fno-schedule-insns -fschedule-insns2 -malign-double -fstrict-aliasin
g -pthread -o .libs/fftw_test fftw_test.o test_main.o ../fftw/.libs/libdf
ftw.so -lm -Wl,--rpath -Wl,/home/mivkov/applications/spack/opt/spack/linux
-ubuntu18.04-x86_64/gcc-7.3.0/fftw-2.1.5-wkxg7i7u6rsmzvtllkzob2ge5dx5q4lq/
lib
1626 creating fftw_test
1627 /bin/bash ../libtool --mode=link /home/mivkov/applications/spack/lib/spack
/env/gcc/gcc -O3 -fomit-frame-pointer -fno-schedule-insns -fschedule-insn
s2 -malign-double -fstrict-aliasing -pthread -o rfftw_test rfftw_test.o
test_main.o ../rfftw/libdrfftw.la ../fftw/libdfftw.la -lm
1628 /home/mivkov/applications/spack/lib/spack/env/gcc/gcc -O3 -fomit-frame-poi
nter -fno-schedule-insns -fschedule-insns2 -malign-double -fstrict-aliasin
g -pthread -o .libs/rfftw_test rfftw_test.o test_main.o ../rfftw/.libs/li
bdrfftw.so ../fftw/.libs/libdfftw.so -lm -Wl,--rpath -Wl,/home/mivkov/appl
ications/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.3.0/fftw-2.1.5-wkx
g7i7u6rsmzvtllkzob2ge5dx5q4lq/lib
>> 1629 ../rfftw/.libs/libdrfftw.so: undefined reference to `fftw_reverse_int_arra
y'
>> 1630 collect2: error: ld returned 1 exit status
1631 Makefile:212: recipe for target 'rfftw_test' failed
>> 1632 make[1]: *** [rfftw_test] Error 1
1633 make[1]: Leaving directory '/tmp/mivkov/spack-stage/spack-stage-R5BBIO/fft
w-2.1.5/double/tests'
1634 Makefile:214: recipe for target 'all-recursive' failed
>> 1635 make: *** [all-recursive] Error 1
See build log for details:
/home/mivkov/applications/spack/var/spack/stage/fftw-2.1.5-wkxg7i7u6rsmzvtllkzob2ge5dx5q4lq/fftw-2.1.5/spack-build.out
So I decided to manually add FFTW 2.1.5 to spack and lmod:
First download FFTW 2:
$ wget http://www.fftw.org/fftw-2.1.5.tar.gz
Then untar it:
$ tar -xvf fftw-2.1.5.tar.gz
Next decide how to name the directory correctly. I put it where the other FFTW libraries are, which I installed with SPACK. You can check where that is by looking at $ echo $FFTW_ROOT.
For me, it was /home/mivkov/applications/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.3.0/fftw-3.3.8-grbvci4ohu36z4qyg6odi5k5fwt7zi77, so I will put it in /home/mivkov/applications/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.3.0/fftw-2.1.5-aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa
Apparently spack uses 32 character long hashes to identify the installs, so just add 32 a’s to the directory name or whatever you want. I’m just an instruction, not the police.
This particular install is with the openmpi library loaded, and later I repeat all the steps with mpich. That’s why I added ‘openmpi’ to the directory name. Make sure you loaded the correct MPI version.
Just using the configure and make for the FFTW2 library might fail to create the documentation; FFTW2 probably relies on some old version of texinfo. But it looks like you can safely ignore that. Let’s be honest, none of us is gonna look for the dox in these directories.
The error I was getting looked like this:
/bin/bash ../mkinstalldirs /home/mivkov/applications/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.3.0/fftw-2.1.5-aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa/include
/usr/bin/install -c -m 644 drfftw.h /home/mivkov/applications/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.3.0/fftw-2.1.5-aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa/include/drfftw.h
make[2]: Leaving directory '/home/mivkov/applications/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.3.0/fftw-2.1.5-aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa/rfftw'
make[1]: Leaving directory '/home/mivkov/applications/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.3.0/fftw-2.1.5-aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa/rfftw'
Making install in tests
make[1]: Entering directory '/home/mivkov/applications/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.3.0/fftw-2.1.5-aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa/tests'
make[2]: Entering directory '/home/mivkov/applications/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.3.0/fftw-2.1.5-aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa/tests'
make[2]: Nothing to be done for 'install-exec-am'.
make[2]: Nothing to be done for 'install-data-am'.
make[2]: Leaving directory '/home/mivkov/applications/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.3.0/fftw-2.1.5-aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa/tests'
make[1]: Leaving directory '/home/mivkov/applications/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.3.0/fftw-2.1.5-aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa/tests'
Making install in doc
make[1]: Entering directory '/home/mivkov/applications/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.3.0/fftw-2.1.5-aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa/doc'
/bin/bash /home/mivkov/applications/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.3.0/fftw-2.1.5-aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa/missing --run makeinfo -I . \
-o fftw.info `test -f 'fftw.texi' || echo './'`fftw.texi
fftw.texi:49: misplaced {
fftw.texi:49: misplaced }
fftw.texi:51: misplaced {
fftw.texi:51: misplaced }
fftw.texi:52: misplaced {
fftw.texi:52: misplaced }
Makefile:188: recipe for target 'fftw.info' failed
make[1]: *** [fftw.info] Error 1
make[1]: Leaving directory '/home/mivkov/applications/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.3.0/fftw-2.1.5-aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa/doc'
Makefile:214: recipe for target 'install-recursive' failed
make: *** [install-recursive] Error 1
Easiest way to bypass it is to remove doc from the SUBDIRS variable in the Makefile that configure creates. Also, to install both single and double precision libraries, we’ll have to configure and compile the library twice, once using --enable-float, once not. To have both libraries simultaneously, we need to add --enable-type-prefix. To save some work and thinking, just pack the following code into a bash script and execute it. Don’t forget to adapt the FFTW2_ROOT appropriately to your situation.
#!/bin/bash
FFTW2_ROOT="/home/mivkov/applications/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.3.0/fftw-2.1.5-bbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbb"
make distclean
make uninstall
./configure --enable-float \
--enable-type-prefix \
--enable-threads \
--enable-mpi \
--prefix=$FFTW2_ROOT
sed -i 's/SUBDIRS = fftw rfftw tests doc threads mpi/SUBDIRS = fftw rfftw tests threads mpi/' Makefile
make -j 8
make install
./configure --enable-type-prefix \
--enable-threads \
--enable-mpi \
--prefix=$FFTW2_ROOT
sed -i 's/SUBDIRS = fftw rfftw tests doc threads mpi/SUBDIRS = fftw rfftw tests threads mpi/' Makefile
make -j 8
make install
Adding FFTW 2 to modules and spack¶
Make your life easier and copy the ../fftw-3.3.8-blablabla/.spack directory into your fftw-2.1.5-blabla directory. Then change file by file:
For build.env, you can just copy-paste the file from the fftw-3.3.8-blablabla/.spack directory. Just pay attention that you grab the file from the fftw3 version with the right MPI version.
But you probably can ignore this file completely, as well as build.out.
spec.yaml:
spec:
- fftw:
version: 2.1.5
arch:
platform: linux
platform_os: ubuntu18.04
target: x86_64
compiler:
name: gcc
version: 7.3.0
namespace: builtin
parameters:
double: true
float: true
fma: false
long_double: true
mpi: true
openmp: false
pfft_patches: false
quad: false
simd:
- avx
- avx2
- sse2
cflags: []
cppflags: []
cxxflags: []
fflags: []
ldflags: []
ldlibs: []
dependencies:
mpich:
hash: goluh6hkr5xlspftwizqxlysbdtghk67
type:
- build
- link
hash: grbvci4ohu36z4qyg6odi5k5fwt7zi77
- mpich:
version: 3.2.1
arch:
platform: linux
platform_os: ubuntu18.04
target: x86_64
compiler:
name: gcc
version: 7.3.0
namespace: builtin
parameters:
device: ch3
hydra: true
netmod: tcp
pmi: true
romio: true
verbs: true
cflags: []
cppflags: []
cxxflags: []
fflags: []
ldflags: []
ldlibs: []
hash: goluh6hkr5xlspftwizqxlysbdtghk67
change the hashes and versions appropriately. For me, it looks like this:
spec:
- fftw:
version: 3.3.8
arch:
platform: linux
platform_os: ubuntu18.04
target: x86_64
compiler:
name: gcc
version: 7.3.0
namespace: builtin
parameters:
double: true
float: true
fma: false
long_double: true
mpi: true
openmp: false
pfft_patches: false
quad: false
simd:
- avx
- avx2
- sse2
cflags: []
cppflags: []
cxxflags: []
fflags: []
ldflags: []
ldlibs: []
dependencies:
openmpi:
mpich:
hash: t35vifchtdehybj232idkc4hkcjh4p54
type:
- build
- link
hash: aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa
- openmpi:
version: 3.1.3
arch:
platform: linux
platform_os: ubuntu18.04
target: x86_64
compiler:
name: gcc
version: 7.3.0
namespace: builtin
parameters:
device: ch3
hydra: true
netmod: tcp
pmi: true
romio: true
verbs: true
cflags: []
cppflags: []
cxxflags: []
fflags: []
ldflags: []
ldlibs: []
hash: t35vifchtdehybj232idkc4hkcjh4p54
Then also go and look for the file in $SPACK_ROOT/opt/spack/.spack-db/index.json, copy-paste the entry for fftw 3, and change it appropriately. For me that was
"grbvci4ohu36z4qyg6odi5k5fwt7zi77": {
"explicit": true,
"installation_time": 1541508606.593818,
"ref_count": 0,
"installed": true,
"path": "/home/mivkov/applications/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.3.0/fftw-3.3.8-grbvci4ohu36z4qyg6odi5k5fwt7zi77",
"spec": {
"fftw": {
"version": "3.3.8",
"arch": {
"platform": "linux",
"platform_os": "ubuntu18.04",
"target": "x86_64"
},
"compiler": {
"name": "gcc",
"version": "7.3.0"
},
"namespace": "builtin",
"parameters": {
"double": true,
"float": true,
"fma": false,
"long_double": true,
"mpi": true,
"openmp": false,
"pfft_patches": false,
"quad": false,
"simd": [
"avx",
"avx2",
"sse2"
],
"cflags": [],
"cppflags": [],
"cxxflags": [],
"fflags": [],
"ldflags": [],
"ldlibs": []
},
"dependencies": {
"mpich": {
"hash": "goluh6hkr5xlspftwizqxlysbdtghk67",
"type": [
"build",
"link"
]
}
}
}
}
},
into:
"aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa": {
"explicit": true,
"installation_time": 1541508606.593818,
"ref_count": 0,
"installed": true,
"path": "/home/mivkov/applications/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.3.0/fftw-2.1.5-aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa",
"spec": {
"fftw": {
"version": "2.1.5",
"arch": {
"platform": "linux",
"platform_os": "ubuntu18.04",
"target": "x86_64"
},
"compiler": {
"name": "gcc",
"version": "7.3.0"
},
"namespace": "builtin",
"parameters": {
"double": true,
"float": true,
"fma": false,
"long_double": true,
"mpi": true,
"openmp": false,
"pfft_patches": false,
"quad": false,
"simd": [
"avx",
"avx2",
"sse2"
],
"cflags": [],
"cppflags": [],
"cxxflags": [],
"fflags": [],
"ldflags": [],
"ldlibs": []
},
"dependencies": {
"openmpi": {
"hash": "35vifchtdehybj232idkc4hkcjh4p54",
"type": [
"build",
"link"
]
}
}
}
}
},
Finally, find where the module files for fftw3 are. You can see that by typing module avail and looking in the title. For me it was
$ module avail
------------- /home/mivkov/applications/spack/share/spack/lmod/linux-ubuntu18.04-x86_64/mpich/3.2.1-goluh6h/Core -------------
fftw/3.3.8 (L) grackle/3.1 (L) hdf5/1.10.4 (L) parmetis/4.0.3 (L)
----------------------- /home/mivkov/applications/spack/share/spack/lmod/linux-ubuntu18.04-x86_64/Core -----------------------
cmake/3.12.3 git/2.17.1 jemalloc/4.5.0 (L) metis/5.1.0 (L) tcl/8.6.8
cuda/10.0.130 gsl/2.5 (L) libtool/2.4.6 mpich/3.2.1 (L) texinfo/5.1
diffutils/3.6 hdf/4.2.13 lmod/7.8 openmpi/3.1.3 texinfo/6.5 (D)
findutils/4.6.0 hwloc/1.11.9 lua/5.3.4 perl/5.26.1 unzip/6.0
Where:
L: Module is loaded
D: Default Module
Use "module spider" to find all possible modules.
Use "module keyword key1 key2 ..." to search for all possible modules matching any of the "keys".
So I see that fftw/3.3.8 with mpich is in /home/mivkov/applications/spack/share/spack/lmod/linux-ubuntu18.04-x86_64/mpich/3.2.1-goluh6h/Core.
Go to the directory of the appropriate MPI version you used, copy-pase the 3.3.8.lua file to 2.1.5.lua file, then search and replace all 3.3.8 with 2.1.5 and the hashes you set.
Finally, reaload the module tree to see the changes:
spack module tcl refresh -y
Now you should see fftw/2.1.5 when using module avail.
Page last edited 2019-10-22