def test_internal_mpi():
import pickle
import sys
import os
import subprocess
from physcraper import ConfigObj, PhyscraperScrape, IdDicts
from mpi4py import MPI
# set up until test
workdir = "tests/output/test_mpi_raxml"
absworkdir = os.path.abspath(workdir)
conf = ConfigObj("tests/data/test.config", interactive=False)
#load data
data_obj = pickle.load(open("tests/data/precooked/tiny_dataobj.p", 'rb'))
data_obj.workdir = absworkdir
ids = IdDicts(conf, workdir=data_obj.workdir)
ids.acc_ncbi_dict = pickle.load(
open("tests/data/precooked/tiny_acc_map.p", "rb"))
scraper = PhyscraperScrape(data_obj, ids)
blast_dir = "tests/data/precooked/fixed/tte_blast_files"
scraper._blasted = 1
# run needed functions
scraper.read_blast_wrapper(blast_dir=blast_dir)
scraper.remove_identical_seqs()
scraper.data.write_papara_files()
scraper.align_query_seqs()
scraper.place_query_seqs()
scraper.est_full_tree()
# scraper.generate_streamed_alignment()
assert os.path.exists("{}/RAxML_bestTree.{}".format(
scraper.workdir, scraper.date))
# scraper.generate_streamed_alignment()
if not os.path.exists("{}/previous_run".format(scraper.workdir)):
os.mkdir("{}/previous_run".format(scraper.workdir))
os.system(
"mv {}/papara_alignment.extended {}/previous_run/papara_alignment.extended"
.format(scraper.workdir, scraper.workdir))
cwd = os.getcwd()
# os.chdir(scraper.workdir)
ntasks = os.environ.get('SLURM_NTASKS_PER_NODE')
nnodes = os.environ.get("SLURM_JOB_NUM_NODES")
print(nnodes, ntasks)
env_var = int(nnodes) * int(ntasks)
#env_var = os.environ.get('SLURM_JOB_CPUS_PER_NODE', 7)
print(env_var)
assert os.path.exists("{}/previous_run/papara_alignment.extended".format(
scraper.workdir))
with cd(scraper.workdir):
print("run with mpi")
subprocess.call([
"mpiexec", "-n", "{}".format(env_var), "raxmlHPC-MPI-AVX2", "-m",
"GTRCAT", "-s", "{}/previous_run/papara_alignment.extended".format(
scraper.workdir), "-p", "1", "-f", "a", "-x", "1", "-#",
"autoMRE", "-n", "all{}".format(scraper.date)
])
