wham exited with error code 2

[gongshuai0606]

Hi, thanks for the good implementation. However, when I run the example.py, I encountered the error: "wham exited with error code 2"

[dnlbauer]

Hey, does the issue still exists? I might be able to help if you provide a bit more details: Can you show your implementation at what software you are using for wham?

[gongshuai0606]

Hey, does the issue still exists? I might be able to help if you provide a bit more details: Can you show your implementation at what software you are using for wham?

Thanks for your reply. I installed wham-2d according to the link "http://membrane.urmc.rochester.edu/sites/default/files/wham/doc.html" in line 69 of adaptiveumbrella/adaptiveumbrella/wham2d.py

cd wham-2d`
make clean
make

then run the example.py

import os
from copy import deepcopy
import matplotlib.pyplot as plt
import numpy as np
import sys
from adaptiveumbrella.wham2d import WHAM2DRunner
sys.path.append('..')
class MyUmbrellaRunner(WHAM2DRunner):
    def __init__(self):
        WHAM2DRunner.__init__(self)
    cum_frames = [0]
    def after_run_hook(self):
        filename = "tmp/pmf_{}.pdf".format("%02d" % self.num_iterations)
        print("Writing new pmf to {}".format(filename))
        pmf_to_plot = deepcopy(self.pmf)
        pmf_to_plot[pmf_to_plot < 0] = None
        pmf_to_plot[self.sample_list == 0] = None
        pmf_to_plot = pmf_to_plot.T
        self.cum_frames.append(len(self.sample_list[self.sample_list > 0]))
        fig, (ax0, ax1) = plt.subplots(ncols=2)
        im = ax0.imshow(pmf_to_plot, origin='lower', cmap='jet')
        cb = fig.colorbar(im, ax=ax0, orientation='horizontal', pad=0.15)
        cb.set_label("kJ/mol")
        ax1.plot(self.cum_frames, linewidth=0.5, marker="o", color='black')
        ax1.set_xlabel("Cycles")
        ax1.set_ylabel("Number of umbrella Windows")
        # ticks = [(x,x) for x in [-3, -2, -1, 0, 1, 2, 3]]
        # tick_positions = [ self._get_index_for_lambdas(x)[0] for x in ticks ]
        # tick_labels = [ str(x[0]) for x in ticks ]
        # ax0.set_yticks(tick_positions)
        # ax0.set_yticklabels(tick_labels)
        # ax0.set_xticks(tick_positions)
        # ax0.set_xticklabels(tick_labels)
        ax0.set_ylabel("$\phi$")
        ax0.set_xlabel("$\psi$")
        fig.subplots_adjust(wspace=.5)
        plt.savefig(filename, bbox_inches='tight', dpi=200)
        os.system("cp {} {}".format(filename, "tmp/pmf_current.pdf"))
    def simulate_frames(self, lambdas, frames):
        print("{} new simulations:".format(len(lambdas)))
        counter = 0
        if not os.path.exists("tmp"):
            os.mkdir('tmp')
        threads = []
        for f in lambdas:
            counter += 1
            print("{}) Simulate lambda1={}, lambda2={}".format(counter, *f))
            command = "bash data/sim.sh {} {} 2>&1 > tmp/run.log".format(*f)
            # print("Running {}".format(command))
            os.system(command)
runner = MyUmbrellaRunner()
runner.WHAM_EXEC = "/home/user/Documents/gs/wham/wham-2d/wham-2d"
runner.whamconfig = {
    'Px': 'pi',
    'hist_min_x': -3,
    'hist_max_x': 3,
    'num_bins_x': 100,
    'Py': 'pi',
    'hist_min_y': -3,
    'hist_max_y': 3,
    'num_bins_y': 100,
    'tolerance': 0.1,
    'fc_x': 100,
    'fc_y': 100,
    'temperature': None,
    'mask': None
}
runner.cvs = np.array([
    (-3, 3, 0.2),
    (-3, 3, 0.2),
])
runner.cvs_init = (0, 0)
runner.E_min = 5
runner.E_max = 100
runner.E_incr = 10
runner.max_iterations = 1
runner.run()

It returned the error:

/home/user/anaconda3/envs/pytorch1.10/bin/python /home/user/Documents/gs/adaptiveumbrella/examples/example.py 
np.shape(windows) (30,)
np.shape(windows) (30,)
~~~~~~~~~~~~~~~ Iteration 1/1 ~~~~~~~~~~~~~~~~
Energy: 5
Running simulations
9 new simulations:
1) Simulate lambda1=-0.2, lambda2=-0.2
2) Simulate lambda1=-0.2, lambda2=0.0
3) Simulate lambda1=-0.2, lambda2=0.2
4) Simulate lambda1=0.0, lambda2=-0.2
5) Simulate lambda1=0.0, lambda2=0.0
6) Simulate lambda1=0.0, lambda2=0.2
7) Simulate lambda1=0.2, lambda2=-0.2
8) Simulate lambda1=0.2, lambda2=0.0
9) Simulate lambda1=0.2, lambda2=0.2
Calculating new PMF
wham exited with error code 2
Process finished with exit code 1

the simulation is performed by gromacs-2018.8

[dnlbauer]

One thing you could try is setting runner.verbose=True. This will print the generated wham-2d command before executing it. This way you can try to run the command manually and see if the error is related to Wham or to this python library.

Unfortunately I do not know what error code 2 means.

Hope this helps!

10 Jun 2023 14:49:38 gongshuai0606 @.***>:

Hey, does the issue still exists? I might be able to help if you provide a bit more details: Can you show your implementation at what software you are using for wham?

Thanks for your reply. I installed wham-2d according to the link "http://membrane.urmc.rochester.edu/sites/default/files/wham/doc.html" in line 69 of adaptiveumbrella/adaptiveumbrella/wham2d.py cd wham-2d make clean make

then run the example.py `#!/usr/bin/env python3 import os from copy import deepcopy

import matplotlib.pyplot as plt import numpy as np

import sys

from adaptiveumbrella.wham2d import WHAM2DRunner

sys.path.append('..')

class MyUmbrellaRunner(WHAM2DRunner):

*def init(self): WHAM2DRunner.init(self)

cum_frames = [0]

def after_runhook(self): filename = "tmp/pmf{}.pdf".format("%02d" % self.num_iterations) print("Writing new pmf to {}".format(filename)) pmf_to_plot = deepcopy(self.pmf) pmf_to_plot[pmf_to_plot < 0] = None pmf_to_plot[self.sample_list == 0] = None pmf_to_plot = pmf_to_plot.T

self.cum_frames.append(len(self.sample_list[self.sample_list > 0]))

fig, (ax0, ax1) = plt.subplots(ncols=2)
im = ax0.imshow(pmf_to_plot, origin='lower', cmap='jet')
cb = fig.colorbar(im, ax=ax0, orientation='horizontal', pad=0.15)
cb.set_label("kJ/mol")

ax1.plot(self.cum_frames, linewidth=0.5, marker="o", color='black')
ax1.set_xlabel("Cycles")
ax1.set_ylabel("Number of umbrella Windows")

# ticks = [(x,x) for x in [-3, -2, -1, 0, 1, 2, 3]]
# tick_positions = [ self._get_index_for_lambdas(x)[0] for x in ticks ]
# tick_labels = [ str(x[0]) for x in ticks ]
# ax0.set_yticks(tick_positions)
# ax0.set_yticklabels(tick_labels)
# ax0.set_xticks(tick_positions)
# ax0.set_xticklabels(tick_labels)
ax0.set_ylabel("$\phi$")
ax0.set_xlabel("$\psi$")

fig.subplots_adjust(wspace=.5)

plt.savefig(filename, bbox_inches='tight', dpi=200)
os.system("cp {} {}".format(filename, "tmp/pmf_current.pdf"))

def simulate_frames(self, lambdas, frames): print("{} new simulations:".format(len(lambdas))) counter = 0

if not os.path.exists("tmp"):
    os.mkdir('tmp')

threads = []
for f in lambdas:
    counter += 1
    print("{}) Simulate lambda1={}, lambda2={}".format(counter, *f))
    command = "bash data/sim.sh {} {} 2>&1 > tmp/run.log".format(*f)
    # print("Running {}".format(command))
    os.system(command)

* runner = MyUmbrellaRunner() runner.WHAM_EXEC = "/home/user/Documents/gs/wham/wham-2d/wham-2d" runner.whamconfig = { 'Px': 'pi', 'hist_min_x': -3, 'hist_max_x': 3, 'num_bins_x': 100, 'Py': 'pi', 'hist_min_y': -3, 'hist_max_y': 3, 'num_bins_y': 100, 'tolerance': 0.1, 'fc_x': 100, 'fc_y': 100, 'temperature': None, 'mask': None }

runner.cvs = np.array([ (-3, 3, 0.2), (-3, 3, 0.2), ]) runner.cvs_init = (0, 0) runner.E_min = 5 runner.E_max = 100 runner.E_incr = 10 runner.max_iterations = 1

runner.run()`

It returned the error: `/home/user/anaconda3/envs/pytorch1.10/bin/python /home/user/Documents/gs/adaptiveumbrella/examples/example.py np.shape(windows) (30,) np.shape(windows) (30,)

*Energy: 5 Running simulations 9 new simulations: 1) Simulate lambda1=-0.2, lambda2=-0.2 2) Simulate lambda1=-0.2, lambda2=0.0 3) Simulate lambda1=-0.2, lambda2=0.2 4) Simulate lambda1=0.0, lambda2=-0.2 5) Simulate lambda1=0.0, lambda2=0.0 6) Simulate lambda1=0.0, lambda2=0.2 7) Simulate lambda1=0.2, lambda2=-0.2 8) Simulate lambda1=0.2, lambda2=0.0 9) Simulate lambda1=0.2, lambda2=0.2 Calculating new PMF wham exited with error code 2

Process finished with exit code 1`

the simulation is performed by gromacs-2018.8 * — Reply to this email directly, view it on GitHub[https://github.com/dnlbauer/adaptiveumbrella/issues/2#issuecomment-1585652126], or unsubscribe[https://github.com/notifications/unsubscribe-auth/ABDZB4TKPAGYHAHNQIOUIV3XKRUNVANCNFSM6AAAAAAYUCKFPA]. You are receiving this because you commented.[Tracking image][https://github.com/notifications/beacon/ABDZB4WS5ORGF34GYEU3XIDXKRUNVA5CNFSM6AAAAAAYUCKFPCWGG33NNVSW45C7OR4XAZNMJFZXG5LFINXW23LFNZ2KUY3PNVWWK3TUL5UWJTS6QMQZ4.gif]