Commit 7b039308 authored by Yakubov, Sergey's avatar Yakubov, Sergey
Browse files

Merge branch 'switch-to-mantid-3.12' into 'main' 

Switch to mantid 6.12

See merge request ndip/tool-sources/topaz/topaz-reduction!2
parents c79a815a 8ef153a1

.gitlab-ci.yml

+1 −1
Original line number Diff line number Diff line
@@ -20,7 +20,7 @@ after_script: 
build-image:

  stage: build

  variables:

    TAG: "0.3"

    TAG: "0.4"

    FORCE_TAGS: "false"

  when: manual

  script:

dockerfiles/Dockerfile

+11 −14
Original line number Diff line number Diff line 
FROM --platform=amd64 ubuntu:22.04

FROM --platform=amd64 regproxy.ornl.gov/hub_proxy/mambaorg/micromamba:2.0-ubuntu22.04 AS source



RUN DEBIAN_FRONTEND="noninteractive" apt-get update && apt-get -y install tzdata

RUN micromamba create --yes -n mantid -c conda-forge -c mantid python=3.10 mantid=6.12.0 muparser=2.3.4 matplotlib



RUN apt-get update && apt-get install -y wget xz-utils libglu1-mesa-dev

USER root



RUN wget https://github.com/mantidproject/mantid/releases/download/v6.7.0/mantidworkbench-6.7.0.tar.xz



RUN tar -xvf ./mantidworkbench-6.7.0.tar.xz



RUN ln -s /mantidworkbench/bin/python /mantidworkbench/bin/mantidpython



ENV PATH=$PATH:/mantidworkbench/bin

ENV PYTHONPATH=$PYTHONPATH:/topaz/lib/ISAW_PythonSources/Lib:/topaz/lib/Python3Library

ENV PYTHONPATH=/topaz/lib/ISAW_PythonSources/Lib:/topaz/lib/Python3Library



COPY mantid.local.properties /etc/mantid.local.properties



COPY /data /topaz/data

COPY /src /topaz/app

COPY /lib /topaz/lib

COPY ./data /topaz/data

COPY ./src /topaz/app

COPY ./lib /topaz/lib

RUN ln -s /topaz/app /app



RUN mkdir /.mantid && chmod og+rwX -R /topaz /.mantid
@@ -26,4 +19,8 @@ ENV SNS_TOPAZ_SHARED_FOLDER="/topaz/data" 


WORKDIR /app



ENTRYPOINT [ "micromamba", "run", "-n", "mantid" ]

src/topaz_reduction.py

+141 −129
Original line number Diff line number Diff line
@@ -23,13 +23,13 @@ 
# ********************************************************************************************

#

import os

import subprocess

import sys

import threading

import time

import math

import numpy as np

from operator import itemgetter

from itertools import groupby



# sys.path.insert(0,"/opt/mantidnightly/bin")

# sys.path.insert(0,"/opt/mantidnightly/lib")
@@ -37,8 +37,8 @@ import ReduceDictionary 


from mantid.simpleapi import *

from mantid.kernel import *

from mantid.geometry import PointGroupFactory, SpaceGroupFactory, UnitCell, Goniometer

from mantid import config



config['Q.convention'] = "Crystallography"

DownloadInstrument(ForceUpdate=True)
@@ -60,7 +60,6 @@ from spectrumCalc import * 
from spectrum2 import *

from absor_sphere import *





print("API Version")

print(apiVersion())
@@ -297,19 +296,25 @@ print('\nCompleted calculation of linear absorption coefficients\n') 
# how the the list of runs will be processed in parallel. 

print("\n*********************************************************************************")

print("************** Start Peak Integration *******************************************")





#

# ProcessThread is a simple local class.  Each instance of ProcessThread is 

# a thread that starts a command line process to reduce one run.

#

class ProcessThread(threading.Thread):

   command = ""

    def __init__(self):

        super().__init__()

        self.return_code = None



    def setCommand(self, command=""):

        self.command = command



    def run(self):

      print(('STARTING PROCESS: ' + self.command))

      os.system( self.command )

        print('STARTING PROCESS:', self.command)

        res = subprocess.run(self.command, shell=True)

        self.return_code = res.returncode





# -------------------------------------------------------------------------

#
@@ -321,7 +326,7 @@ list=[] 
index = 0

for r_num in run_nums:

    list.append(ProcessThread())

  cmd = 'mantidpython -u ' + reduce_one_run_script + ' ' + config_file_name + ' ' + str(r_num)

    cmd = 'python -u ' + reduce_one_run_script + ' ' + config_file_name + ' ' + str(r_num)

    if slurm_queue_name is not None:

        console_file = output_directory + "/" + str(r_num) + "_output.txt"

        cmd = 'srun -p ' + slurm_queue_name + \
@@ -335,6 +340,7 @@ for r_num in run_nums: 
#

all_done = False

active_list = []

return_codes = []

while not all_done:

    if (len(list) > 0 and len(active_list) < max_processes):

        thread = list[0]
@@ -345,6 +351,7 @@ while not all_done: 
    for thread in active_list:

        if not thread.is_alive():

            active_list.remove(thread)

            return_codes.append(thread.return_code)

    if len(list) == 0 and len(active_list) == 0:

        all_done = True
@@ -353,3 +360,8 @@ print("****************************** All DONE ********************************* 
print("**************************************************************************************\n")



print('Config file: ' + config_file_name)



for code in return_codes:

    if code != 0:

        print('Finished with errors')

        sys.exit(1)