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Merge pull request #20 from sfiligoi/igor_default_fp32
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Change default method precision to fp32, and add explicit _fp64 equivalent
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@sfiligoi
sfiligoi authored Dec 1, 2022
2 parents c7783a8 + f770850 commit 0257c7c
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Showing 4 changed files with 38 additions and 20 deletions.
15 changes: 10 additions & 5 deletions .github/workflows/main.yml
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Expand Up @@ -103,30 +103,35 @@ jobs:
./compare_unifrac_matrix.py test500.weighted_unnormalized_fp32.h5 t1.h5 1.e-5
./compare_unifrac_pcoa.py test500.weighted_unnormalized_fp32.h5 t1.h5 3 0.1
rm -f t1.h5
# retry with default precision handling
time ssu -m weighted_unnormalized -i test500.biom -t test500.tre --pcoa 4 -r hdf5 -o t1.h5
./compare_unifrac_matrix.py test500.weighted_unnormalized_fp32.h5 t1.h5 1.e-5
./compare_unifrac_pcoa.py test500.weighted_unnormalized_fp32.h5 t1.h5 3 0.1
rm -f t1.h5
time ssu -f -m weighted_unnormalized_fp32 -i test500.biom -t test500.tre --pcoa 4 -r hdf5_fp32 -o t1.h5
# matrrix will be different, but PCOA similar
./compare_unifrac_pcoa.py test500.weighted_unnormalized_fp32.h5 t1.h5 3 0.1
rm -f t1.h5
time ssu -m weighted_unnormalized -i test500.biom -t test500.tre --pcoa 4 -r hdf5_fp64 -o t1.h5
time ssu -m weighted_unnormalized_fp64 -i test500.biom -t test500.tre --pcoa 4 -r hdf5_fp64 -o t1.h5
# minimal precision loss between fp32 and fp64
./compare_unifrac_matrix.py test500.weighted_unnormalized_fp32.h5 t1.h5 1.e-5
./compare_unifrac_pcoa.py test500.weighted_unnormalized_fp32.h5 t1.h5 3 0.1
rm -f t1.h5
# weighted_normalized
time ssu -f -m weighted_normalized_fp32 -i test500.biom -t test500.tre --pcoa 4 -r hdf5_fp32 -o t1.h5
time ssu -f -m weighted_normalized -i test500.biom -t test500.tre --pcoa 4 -r hdf5_fp32 -o t1.h5
./compare_unifrac_matrix.py test500.weighted_normalized_fp32.f.h5 t1.h5 1.e-5
./compare_unifrac_pcoa.py test500.weighted_normalized_fp32.f.h5 t1.h5 3 0.1
rm -f t1.h5
time ssu -f -m weighted_normalized -i test500.biom -t test500.tre --pcoa 4 -r hdf5_fp64 -o t1.h5
time ssu -f -m weighted_normalized_fp64 -i test500.biom -t test500.tre --pcoa 4 -r hdf5_fp64 -o t1.h5
./compare_unifrac_matrix.py test500.weighted_normalized_fp32.f.h5 t1.h5 1.e-5
./compare_unifrac_pcoa.py test500.weighted_normalized_fp32.f.h5 t1.h5 3 0.1
rm -f t1.h5
# unweighted
time ssu -f -m unweighted_fp32 -i test500.biom -t test500.tre --pcoa 4 -r hdf5_fp32 -o t1.h5
time ssu -f -m unweighted -i test500.biom -t test500.tre --pcoa 4 -r hdf5_fp32 -o t1.h5
./compare_unifrac_matrix.py test500.unweighted_fp32.f.h5 t1.h5 1.e-5
./compare_unifrac_pcoa.py test500.unweighted_fp32.f.h5 t1.h5 3 0.1
rm -f t1.h5
time ssu -f -m unweighted -i test500.biom -t test500.tre --pcoa 4 -r hdf5_fp64 -o t1.h5
time ssu -f -m unweighted_fp64 -i test500.biom -t test500.tre --pcoa 4 -r hdf5_fp64 -o t1.h5
./compare_unifrac_matrix.py test500.unweighted_fp32.f.h5 t1.h5 1.e-5
./compare_unifrac_pcoa.py test500.unweighted_fp32.f.h5 t1.h5 3 0.1
rm -f t1.h5
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1 change: 1 addition & 0 deletions README.md
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Expand Up @@ -135,6 +135,7 @@ The methods can be used directly through the command line after install:
-i The input BIOM table.
-t The input phylogeny in newick.
-m The method, [unweighted | weighted_normalized | weighted_unnormalized | generalized |
unweighted_fp64 | weighted_normalized_fp64 | weighted_unnormalized_fp64 | generalized_fp64 |
unweighted_fp32 | weighted_normalized_fp32 | weighted_unnormalized_fp32 | generalized_fp32].
-o The output distance matrix.
-a [OPTIONAL] Generalized UniFrac alpha, default is 1.
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32 changes: 21 additions & 11 deletions src/api.cpp
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Expand Up @@ -43,15 +43,23 @@
return err; \
}

#define SET_METHOD(requested_method, err) Method method; \
if(std::strcmp(requested_method, "unweighted") == 0) \
method = unweighted; \
else if(std::strcmp(requested_method, "weighted_normalized") == 0) \
method = weighted_normalized; \
else if(std::strcmp(requested_method, "weighted_unnormalized") == 0) \
method = weighted_unnormalized; \
else if(std::strcmp(requested_method, "generalized") == 0) \
method = generalized; \
#define SET_METHOD(requested_method, err) Method method; \
if(std::strcmp(requested_method, "unweighted") == 0) \
method = unweighted_fp32; \
else if(std::strcmp(requested_method, "weighted_normalized") == 0) \
method = weighted_normalized_fp32; \
else if(std::strcmp(requested_method, "weighted_unnormalized") == 0) \
method = weighted_unnormalized_fp32; \
else if(std::strcmp(requested_method, "generalized") == 0) \
method = generalized_fp32; \
else if(std::strcmp(requested_method, "unweighted_fp64") == 0) \
method = unweighted; \
else if(std::strcmp(requested_method, "weighted_normalized_fp64") == 0) \
method = weighted_normalized; \
else if(std::strcmp(requested_method, "weighted_unnormalized_fp64") == 0) \
method = weighted_unnormalized; \
else if(std::strcmp(requested_method, "generalized_fp64") == 0) \
method = generalized; \
else if(std::strcmp(requested_method, "unweighted_fp32") == 0) \
method = unweighted_fp32; \
else if(std::strcmp(requested_method, "weighted_normalized_fp32") == 0) \
Expand Down Expand Up @@ -166,10 +174,12 @@ void initialize_mat_no_biom(mat_t* &result, char** sample_ids, unsigned int n_sa
}

inline compute_status is_fp64_method(const std::string &method_string, bool &fp64) {
if ((method_string=="unweighted_fp32") || (method_string=="weighted_normalized_fp32") || (method_string=="weighted_unnormalized_fp32") || (method_string=="generalized_fp32")) {
if ((method_string=="unweighted") || (method_string=="weighted_normalized") || (method_string=="weighted_unnormalized") || (method_string=="generalized")) {
fp64 = false;
} else if ((method_string=="unweighted") || (method_string=="weighted_normalized") || (method_string=="weighted_unnormalized") || (method_string=="generalized")) {
} else if ((method_string=="unweighted_fp64") || (method_string=="weighted_normalized_fp64") || (method_string=="weighted_unnormalized_fp64") || (method_string=="generalized_fp64")) {
fp64 = true;
} else if ((method_string=="unweighted_fp32") || (method_string=="weighted_normalized_fp32") || (method_string=="weighted_unnormalized_fp32") || (method_string=="generalized_fp32")) {
fp64 = false;
} else {
return unknown_method;
}
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10 changes: 6 additions & 4 deletions src/su.cpp
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Expand Up @@ -20,7 +20,9 @@ void usage() {
std::cout << std::endl;
std::cout << " -i\t\tThe input BIOM table." << std::endl;
std::cout << " -t\t\tThe input phylogeny in newick." << std::endl;
std::cout << " -m\t\tThe method, [unweighted | weighted_normalized | weighted_unnormalized | generalized | unweighted_fp32 | weighted_normalized_fp32 | weighted_unnormalized_fp32 | generalized_fp32]." << std::endl;
std::cout << " -m\t\tThe method, [unweighted | weighted_normalized | weighted_unnormalized | generalized |" << std::endl;
std::cout << " unweighted_fp64 | weighted_normalized_fp64 | weighted_unnormalized_fp64 | generalized_fp64 |" << std::endl;
std::cout << " unweighted_fp32 | weighted_normalized_fp32 | weighted_unnormalized_fp32 | generalized_fp32]." << std::endl;
std::cout << " -o\t\tThe output distance matrix." << std::endl;
std::cout << " -a\t\t[OPTIONAL] Generalized UniFrac alpha, default is 1." << std::endl;
std::cout << " -f\t\t[OPTIONAL] Bypass tips, reduces compute by about 50%." << std::endl;
Expand Down Expand Up @@ -430,10 +432,10 @@ Format get_format(const std::string &format_string, const std::string &method_st
} else if (format_string == "hdf5_fp64") {
format_val = format_hdf5_fp64;
} else if (format_string == "hdf5") {
if ((method_string=="unweighted_fp32") || (method_string=="weighted_normalized_fp32") || (method_string=="weighted_unnormalized_fp32") || (method_string=="generalized_fp32"))
format_val = format_hdf5_fp32;
else
if ((method_string=="unweighted_fp64") || (method_string=="weighted_normalized_fp64") || (method_string=="weighted_unnormalized_fp64") || (method_string=="generalized_fp64"))
format_val = format_hdf5_fp64;
else
format_val = format_hdf5_fp32;
}

return format_val;
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