Issues building the released version of PhoSim from BitBucket

Support
,
#1

I was trying to build the PhoSim package from https://bitbucket.org/phosim/phosim_release/wiki/Home, but I’ve run into some issues. It seems like the package as released is not designed to be built on its own, or maybe I’m missing some files? I cloned the repo, cd'ed, and ran make. I got some errors about commands and files not being found. It looks like some variables used in the Makefile are not defined, and the bin/setup script that is perhaps supposed to set them is not found (because it is .gitignore'd).

I’m really just looking to create a single (highly oversampled) representative PSF for LSST for use in some data mocking, so if anyone has PhoSim installed and knows how to produce that, I’d be much obliged! (Of course, I’d like to be able to figure this out as well :slight_smile: )

Here’s the full output:

10:01:11 tanuki:deblend jlong$ git clone https://bitbucket.org/phosim/phosim_release.git
Cloning into 'phosim_release'...
remote: Counting objects: 19004, done.
remote: Compressing objects: 100% (5208/5208), done.
remote: Total 19004 (delta 13521), reused 18930 (delta 13472)
Receiving objects: 100% (19004/19004), 399.64 MiB | 3.75 MiB/s, done.
Resolving deltas: 100% (13521/13521), done.
Checking connectivity... done.
Checking out files: 100% (1167/1167), done.
10:08:18 tanuki:deblend jlong$ cd phosim_release/
ls
10:08:27 tanuki:phosim_release[master] jlong$ ls
COPYING              data                 source
Doxyfile             default_instcat      test_integration
Makefile             docs                 test_unit
README               examples             tools
ancillary            focalplanelayout.txt validation
bin                  output               validation.py
cleanup              phosim               validation_pipeline
condor               phosim.py            work
configure            raytraceGPU
10:08:33 tanuki:phosim_release[master] jlong$ mate .
10:08:54 tanuki:phosim_release[master] jlong$ make
rm -f source/raytrace/*.o; rm -f source/trim/*.o; rm -f source/e2adc/*.o; rm -f source/instrument/*.o; rm -f source/atmosphere/*.o ; rm -f source/ancillary/*.o
csh -c "source bin/setup ; cd source/raytrace ; make; mv raytrace ../../bin/."
[1] 13974
bin/setup: No such file or directory.
make[1]: Entering directory '/astro/ferguson1/jlong/deblend/phosim_release/source/raytrace'
g -O3 -ffast-math -Wall -c -I -I -I ../ main.cpp -o main.o
make[1]: g: Command not found
Makefile:14: recipe for target 'main.o' failed
make[1]: [main.o] Error 127 (ignored)
g -O3 -ffast-math -Wall -c -I -I -I ../ observation.cpp -o observation.o
make[1]: g: Command not found
Makefile:17: recipe for target 'observation.o' failed
make[1]: [observation.o] Error 127 (ignored)
g -O3 -ffast-math -Wall -c -I -I -I ../ image.cpp -o image.o
make[1]: g: Command not found
Makefile:20: recipe for target 'image.o' failed
make[1]: [image.o] Error 127 (ignored)
g -O3 -ffast-math -Wall -c -I -I -I ../ rng_mwc.cpp -o rng_mwc.o
make[1]: g: Command not found
Makefile:23: recipe for target 'rng_mwc.o' failed
make[1]: [rng_mwc.o] Error 127 (ignored)
g -O3 -ffast-math -Wall -c -I -I -I ../ raytrace.cpp -o raytrace.o
make[1]: g: Command not found
Makefile:26: recipe for target 'raytrace.o' failed
make[1]: [raytrace.o] Error 127 (ignored)
g -O3 -ffast-math -Wall -c -I -I -I ../ galaxy.cpp -o galaxy.o
make[1]: g: Command not found
Makefile:29: recipe for target 'galaxy.o' failed
make[1]: [galaxy.o] Error 127 (ignored)
g -O3 -ffast-math -Wall -c -I -I -I ../ dust.cpp -o dust.o
make[1]: g: Command not found
Makefile:32: recipe for target 'dust.o' failed
make[1]: [dust.o] Error 127 (ignored)
g -O3 -ffast-math -Wall -c -I -I -I ../ event.cpp -o event.o
make[1]: g: Command not found
Makefile:35: recipe for target 'event.o' failed
make[1]: [event.o] Error 127 (ignored)
g -O3 -ffast-math -Wall -c -I -I -I ../ grating.cpp -o grating.o
make[1]: g: Command not found
Makefile:68: recipe for target 'grating.o' failed
make[1]: [grating.o] Error 127 (ignored)
g -O3 -ffast-math -Wall -c -I -I -I ../ counter.cpp -o counter.o
make[1]: g: Command not found
Makefile:71: recipe for target 'counter.o' failed
make[1]: [counter.o] Error 127 (ignored)
g -O3 -ffast-math -Wall -c -I -I -I ../ silicon.cpp -o silicon.o
make[1]: g: Command not found
Makefile:38: recipe for target 'silicon.o' failed
make[1]: [silicon.o] Error 127 (ignored)
g -O3 -ffast-math -Wall -c -I -I -I ../ ../ancillary/readtext.cpp -o readtext.o
make[1]: g: Command not found
Makefile:74: recipe for target 'readtext.o' failed
make[1]: [readtext.o] Error 127 (ignored)
g -O3 -ffast-math -Wall -c -I -I -I ../ surface.cpp -o surface.o
make[1]: g: Command not found
Makefile:41: recipe for target 'surface.o' failed
make[1]: [surface.o] Error 127 (ignored)
g -O3 -ffast-math -Wall -c -I -I -I ../ coating.cpp -o coating.o
make[1]: g: Command not found
Makefile:44: recipe for target 'coating.o' failed
make[1]: [coating.o] Error 127 (ignored)
g -O3 -ffast-math -Wall -c -I -I -I ../ perturbation.cpp -o perturbation.o
make[1]: g: Command not found
Makefile:47: recipe for target 'perturbation.o' failed
make[1]: [perturbation.o] Error 127 (ignored)
g -O3 -ffast-math -Wall -c -I -I -I ../ obstruction.cpp -o obstruction.o
make[1]: g: Command not found
Makefile:59: recipe for target 'obstruction.o' failed
make[1]: [obstruction.o] Error 127 (ignored)
g -O3 -ffast-math -Wall -c -I -I -I ../ screen.cpp -o screen.o
make[1]: g: Command not found
Makefile:50: recipe for target 'screen.o' failed
make[1]: [screen.o] Error 127 (ignored)
g -O3 -ffast-math -Wall -c -I -I -I ../ medium.cpp -o medium.o
make[1]: g: Command not found
Makefile:53: recipe for target 'medium.o' failed
make[1]: [medium.o] Error 127 (ignored)
g -O3 -ffast-math -Wall -c -I -I -I ../ air.cpp -o air.o
make[1]: g: Command not found
Makefile:56: recipe for target 'air.o' failed
make[1]: [air.o] Error 127 (ignored)
g -O3 -ffast-math -Wall -c -I -I -I ../ chip.cpp -o chip.o
make[1]: g: Command not found
Makefile:65: recipe for target 'chip.o' failed
make[1]: [chip.o] Error 127 (ignored)
g -O3 -ffast-math -Wall -c -I -I -I ../ contamination.cpp -o contamination.o
make[1]: g: Command not found
Makefile:62: recipe for target 'contamination.o' failed
make[1]: [contamination.o] Error 127 (ignored)
g -O3 -ffast-math -Wall -c -I -I -I ../ fea.cpp -o fea.o
make[1]: g: Command not found
Makefile:77: recipe for target 'fea.o' failed
make[1]: [fea.o] Error 127 (ignored)
main.o observation.o image.o rng_mwc.o raytrace.o galaxy.o dust.o event.o grating.o counter.o silicon.o readtext.o surface.o coating.o perturbation.o obstruction.o screen.o medium.o air.o chip.o contamination.o fea.o -g -O3 -ffast-math -Wall -I -L -lcfitsio -I -L -lfftw3 -lm -lz -o ./raytrace
make[1]: main.o: Command not found
Makefile:10: recipe for target 'raytrace' failed
make[1]: *** [raytrace] Error 127
make[1]: Leaving directory '/astro/ferguson1/jlong/deblend/phosim_release/source/raytrace'
mv: rename raytrace to ../../bin/./raytrace: No such file or directory
[1]  + Done                          alias runidle python3.4 -m idlelib.idle
Makefile:4: recipe for target 'all' failed
make: *** [all] Error 1
How to update a saved catalog to a new format?
#2

Hi Joseph,

I think you forgot to run ./configure in phosim’s home directory.

See the install instructions here

https://bitbucket.org/phosim/phosim_release/wiki/Using%20PhoSim

#3

Ah, how’d I miss that?! I swear I looked for a ./configure… Anyway, much more interesting errors now:

#4

All right, corrected with some tweaks to CFLAGS (per suggestion at http://stackoverflow.com/questions/16352833/linking-with-clang-on-os-x-generates-lots-of-symbol-not-found-errors):

CFLAGS = -g -O3 -ffast-math -Wall -c -I${CFIO_INC_DIR}  -I${FFTW3_INC_DIR} -I ../

becomes

CFLAGS = -stdlib=libc++ -g -O3 -ffast-math -Wall -c -I${CFIO_INC_DIR}  -I${FFTW3_INC_DIR} -I ../