Merge conflicts #2408420
scharlton2 opened this issue · comments
Running with gitlab-runner 15.10.1 (dcfb4b66)
on chs-shared-runners-i-046ce0ed6313[2](https://code.chs.usgs.gov/coupled/phreeqc3/-/jobs/2408420#L2)6747 [3](https://code.chs.usgs.gov/coupled/phreeqc3/-/jobs/2408420#L3)dxCawZT, system ID: s_2635aaf9f0a1
Preparing the "docker+machine" executor
00:07
Using Docker executor with image code.chs.usgs.gov:5001/coupled/containers/buildpack-deps:bionic-scm ...
Authenticating with credentials from job payload (GitLab Registry)
Pulling docker image code.chs.usgs.gov:5001/coupled/containers/buildpack-deps:bionic-scm ...
Using docker image sha256:cbed96d2ebf25728c8b52b136ad931[4](https://code.chs.usgs.gov/coupled/phreeqc3/-/jobs/2408420#L4)cc1dabb3b82f97c633beb27d7b3786b80 for code.chs.usgs.gov:[5](https://code.chs.usgs.gov/coupled/phreeqc3/-/jobs/2408420#L5)001/coupled/containers/buildpack-deps:bionic-scm with digest code.chs.usgs.gov:5001/coupled/containers/buildpack-deps@sha25[6](https://code.chs.usgs.gov/coupled/phreeqc3/-/jobs/2408420#L6):4b53[7](https://code.chs.usgs.gov/coupled/phreeqc3/-/jobs/2408420#L7)16f1b6f2bd3039707fa25a200b793825825f4f7d1adb4e3d534ac0d9d0d ...
Preparing environment
00:01
Running on runner-3dxcawzt-project-4256-concurrent-0 via runner-3dxcawzt-gitlab-runner-1681144741-cbf8231d...
Getting source from Git repository
00:24
Fetching changes with git depth set to 50...
Initialized empty Git repository in /builds/coupled/phreeqc3/.git/
Created fresh repository.
Checking out 60c6d5d0 as detached HEAD (ref is master)...
Skipping Git submodules setup
Executing "step_script" stage of the job script
01:14
Using docker image sha256:cbed96d2ebf25728c8b52b136ad9314cc1dabb3b82f97c633beb27d7b3786b80 for code.chs.usgs.gov:5001/coupled/containers/buildpack-deps:bionic-scm with digest code.chs.usgs.gov:5001/coupled/containers/buildpack-deps@sha256:4b53716f1b6f2bd3039707fa25a200b793825825f4f7d1adb4e3d534ac0d9d0d ...
$ eval $(ssh-agent -s)
Agent pid 14
$ echo "${SSH_PRIVATE_KEY_ENC}" | base64 --decode | tr -d '\r' | ssh-add -
Identity added: (stdin) (darth@empire.com)
$ mkdir -p ~/.ssh
$ chmod 700 ~/.ssh
$ ssh-keyscan ${CI_SERVER_HOST} >> ~/.ssh/known_hosts
# code.chs.usgs.gov:22 SSH-2.0-OpenSSH_7.4
# code.chs.usgs.gov:22 SSH-2.0-OpenSSH_7.4
# code.chs.usgs.gov:22 SSH-2.0-OpenSSH_7.4
$ chmod 644 ~/.ssh/known_hosts
$ git config --global user.email "darth@empire.com"
$ git config --global user.name "Darth Vader"
$ cd ..
$ rm -rf ${CI_PROJECT_NAME}
$ git clone git@${CI_SERVER_HOST}:${CI_PROJECT_PATH}.git
Cloning into 'phreeqc3'...
Warning: Permanently added the ECDSA host key for IP address '10.12.1.165' to the list of known hosts.
remote: warning: ignoring extra bitmap file: '/var/opt/gitlab/git-data/repositories/@pools/[9](https://code.chs.usgs.gov/coupled/phreeqc3/-/jobs/2408420#L9)c/fd/9cfd3c755be26b4e1645918e2a64a26e3d851ede421e0b257f783b443bc443d1.git/objects/pack/multi-pack-index'
Checking out files: 100% (3494/3494), done.
$ cd ${CI_PROJECT_NAME}
$ #!/bin/bash -ex # collapsed multi-line command
remote: warning: ignoring extra bitmap file: '/var/opt/gitlab/git-data/repositories/@pools/aa/e0/aae02129362d611717b6c00ad8d73bf820a0f6d88fca8e515cafe78d3a335965.git/objects/pack/multi-pack-index'
From code.chs.usgs.gov:coupled/subtrees/phreeqc3-doc
* branch master -> FETCH_HEAD
Subtree is already at commit c3ed55b0e443c4ea3b85ecfc4fd8c78416a53321.
From code.chs.usgs.gov:coupled/subtrees/phreeqc3-HTMLversion
* branch master -> FETCH_HEAD
Subtree is already at commit ca6d59b0762e50d66ffbea82f9a63666bf573312.
From code.chs.usgs.gov:coupled/subtrees/phreeqc3-database
* branch master -> FETCH_HEAD
Subtree is already at commit 91aa5fd89b2f211b1dc85020c227df1a35676318.
remote: warning: ignoring extra bitmap file: '/var/opt/gitlab/git-data/repositories/@pools/43/c7/43c727ee4fc7250574d2ef90cfa16626388a10e1b30d36ece1c272953ad2ed9e.git/objects/pack/multi-pack-index'
From code.chs.usgs.gov:coupled/subtrees/phreeqc3-src
* branch master -> FETCH_HEAD
Auto-merging src/tally.cpp
CONFLICT (content): Merge conflict in src/tally.cpp
Auto-merging src/spread.cpp
CONFLICT (content): Merge conflict in src/spread.cpp
Auto-merging src/prep.cpp
CONFLICT (content): Merge conflict in src/prep.cpp
Auto-merging src/pitzer.cpp
CONFLICT (content): Merge conflict in src/pitzer.cpp
Auto-merging src/model.cpp
CONFLICT (content): Merge conflict in src/model.cpp
Auto-merging src/gases.cpp
CONFLICT (content): Merge conflict in src/gases.cpp
Auto-merging src/cl1.cpp
Automatic merge failed; fix conflicts and then commit the result.
Cleaning up project directory and file based variables
00:01
ERROR: Job failed: exit code 1
Forgot to merge in code.chs before merging in #37. Accepted all incoming changes from #37. All were very similar -- mostly things had been deleted in phreeqcrm but only commented out in phreeqc3. To recreate conflicts:
git clone git@github.com:usgs-coupled/phreeqc3.git
git reset --hard e5e03c00
git merge 60c6d5d0239d28ca7733e3d0c181dd4d1f16c563
git --no-pager diff
diff --cc src/gases.cpp
index b373068a,72d8fe12..00000000
--- a/src/gases.cpp
+++ b/src/gases.cpp
@@@ -624,6 -624,7 +624,10 @@@ int Phreeqc:
calc_fixed_volume_gas_pressures(void)
/* ---------------------------------------------------------------------- */
{
++<<<<<<< HEAD
++=======
+ //int n_g = 0;
++>>>>>>> 60c6d5d0239d28ca7733e3d0c181dd4d1f16c563
LDBLE lp;
class rxn_token *rxn_ptr;
class phase *phase_ptr;
@@@ -644,6 -645,7 +648,10 @@@
{
if (!PR && phase_ptr->t_c > 0 && phase_ptr->p_c > 0)
PR = true;
++<<<<<<< HEAD
++=======
+ //n_g++;
++>>>>>>> 60c6d5d0239d28ca7733e3d0c181dd4d1f16c563
}
gas_phase_ptr->Set_total_moles(gas_phase_ptr->Get_total_moles() + gas_unknowns[i]->moles);
}
diff --cc src/model.cpp
index bf8d8fd7,eb5be6ab..00000000
--- a/src/model.cpp
+++ b/src/model.cpp
@@@ -2543,6 -2543,7 +2543,10 @@@ int Phreeqc:
calc_gas_pressures(void)
/* ---------------------------------------------------------------------- */
{
++<<<<<<< HEAD
++=======
+ //int n_g = 0;
++>>>>>>> 60c6d5d0239d28ca7733e3d0c181dd4d1f16c563
LDBLE lp, V_m = 0;
class rxn_token *rxn_ptr;
std::vector<class phase *> phase_ptrs;
@@@ -2575,6 -2576,7 +2579,10 @@@
phase_ptrs.push_back(phase_ptr);
if (!PR && phase_ptr->t_c > 0 && phase_ptr->p_c > 0)
PR = true;
++<<<<<<< HEAD
++=======
+ //n_g++;
++>>>>>>> 60c6d5d0239d28ca7733e3d0c181dd4d1f16c563
}
if (iterations > 2 && gas_phase_ptr->Get_type() == cxxGasPhase::GP_VOLUME)
{
@@@ -3776,6 -3778,7 +3784,10 @@@ residuals(void
int converge;
LDBLE l_toler;
++<<<<<<< HEAD
++=======
+ //LDBLE sum_residual;
++>>>>>>> 60c6d5d0239d28ca7733e3d0c181dd4d1f16c563
LDBLE sinh_constant;
LDBLE sum, sum1;
class master *master_ptr, *master_ptr1, *master_ptr2;
@@@ -3783,6 -3786,7 +3795,10 @@@
int print_fail;
std::vector<LDBLE> cd_psi;
print_fail = FALSE;
++<<<<<<< HEAD
++=======
+ //sum_residual = 0.0;
++>>>>>>> 60c6d5d0239d28ca7733e3d0c181dd4d1f16c563
sigmaddl = 0;
sum = 0;
/*
@@@ -4526,6 -4530,7 +4542,10 @@@
* Store residuals in array
*/
my_array[((size_t)i + 1) * (count_unknowns + 1) - 1] = residual[i];
++<<<<<<< HEAD
++=======
+ //sum_residual += fabs(residual[i]);
++>>>>>>> 60c6d5d0239d28ca7733e3d0c181dd4d1f16c563
}
/*
* Return
diff --cc src/pitzer.cpp
index b71f24d3,35d494fc..00000000
--- a/src/pitzer.cpp
+++ b/src/pitzer.cpp
@@@ -52,6 -52,7 +52,10 @@@ pitzer_tidy(void
const char *string1, *string2;
int i, j, order;
int i0, i1, i2;
++<<<<<<< HEAD
++=======
+ //int count_pos, count_neg, count_neut, count[3], jj;
++>>>>>>> 60c6d5d0239d28ca7733e3d0c181dd4d1f16c563
int count_neut, count[3], jj;
LDBLE z0, z1;
class pitz_param *pzp_ptr;
@@@ -339,21 -340,22 +343,39 @@@
i0 = pitz_params[i]->ispec[0];
i1 = pitz_params[i]->ispec[1];
i2 = pitz_params[i]->ispec[2];
++<<<<<<< HEAD
+ count_neut = 0;
+ for (j = 0; j <= 2; j++)
+ {
+ //if (spec[pitz_params[i]->ispec[j]]->z > 0)
+ //{
+ // count_pos++;
+ //}
++=======
+ //count_pos = count_neg = count_neut = 0;
+ count_neut = 0;
+ for (j = 0; j <= 2; j++)
+ {
+ if (spec[pitz_params[i]->ispec[j]]->z > 0)
+ {
+ //count_pos++;
+ }
++>>>>>>> 60c6d5d0239d28ca7733e3d0c181dd4d1f16c563
if (spec[pitz_params[i]->ispec[j]]->z == 0)
{
count_neut++;
}
++<<<<<<< HEAD
+ //if (spec[pitz_params[i]->ispec[j]]->z < 0)
+ //{
+ // count_neg++;
+ //}
++=======
+ if (spec[pitz_params[i]->ispec[j]]->z < 0)
+ {
+ //count_neg++;
+ }
++>>>>>>> 60c6d5d0239d28ca7733e3d0c181dd4d1f16c563
}
/* All neutral */
if (count_neut == 3)
diff --cc src/prep.cpp
index 0d26ba98,f98d584c..00000000
--- a/src/prep.cpp
+++ b/src/prep.cpp
@@@ -1980,6 -1980,7 +1980,10 @@@ get_list_master_ptrs(const char* cptr,
* Output: space is allocated and a list of master species pointers is
* returned.
*/
++<<<<<<< HEAD
++=======
+ //int j, l, count_list;
++>>>>>>> 60c6d5d0239d28ca7733e3d0c181dd4d1f16c563
int j, l;
char token[MAX_LENGTH];
std::vector<class master*> master_ptr_list;
@@@ -1987,6 -1988,7 +1991,10 @@@
/*
* Make list of master species pointers
*/
++<<<<<<< HEAD
++=======
+ //count_list = 0;
++>>>>>>> 60c6d5d0239d28ca7733e3d0c181dd4d1f16c563
//master_ptr_list = unknown_alloc_master();
master_ptr0 = master_ptr;
if (master_ptr0 == master_ptr->s->primary)
@@@ -2146,6 -2148,7 +2154,10 @@@ mb_for_species_aq(int n
* by coef, usually moles.
* mb_unknowns.coef - coefficient of s[n] in equation or relation
*/
++<<<<<<< HEAD
++=======
+ //int i, j;
++>>>>>>> 60c6d5d0239d28ca7733e3d0c181dd4d1f16c563
int i;
class master *master_ptr;
class unknown *unknown_ptr;
@@@ -2222,6 -2225,7 +2234,10 @@@
*/
if (use.Get_surface_ptr() != NULL && s[n]->type < H2O && dl_type_x != cxxSurface::NO_DL)
{
++<<<<<<< HEAD
++=======
+ //j = 0;
++>>>>>>> 60c6d5d0239d28ca7733e3d0c181dd4d1f16c563
for (i = 0; i < count_unknowns; i++)
{
if (x[i]->type == SURFACE_CB)
@@@ -2233,6 -2237,7 +2249,10 @@@
store_mb_unknowns(unknown_ptr, s_diff_layer[n][charge_ptr->Get_name()].Get_g_moles_address(),
s[n]->z, s_diff_layer[n][charge_ptr->Get_name()].Get_dg_g_moles_address());
++<<<<<<< HEAD
++=======
+ //j++;
++>>>>>>> 60c6d5d0239d28ca7733e3d0c181dd4d1f16c563
}
}
}
diff --cc src/spread.cpp
index 5d7137b5,1f442138..00000000
--- a/src/spread.cpp
+++ b/src/spread.cpp
@@@ -1141,6 -1141,7 +1141,10 @@@ copy_token_tab(std::string& token, cons
* EOL,
* UNKNOWN.
*/
++<<<<<<< HEAD
++=======
+ //int i, return_value;
++>>>>>>> 60c6d5d0239d28ca7733e3d0c181dd4d1f16c563
int return_value;
char c;
/*
@@@ -1180,6 -1181,7 +1184,10 @@@
/*
* Begin copying to token
*/
++<<<<<<< HEAD
++=======
+ //i = 0;
++>>>>>>> 60c6d5d0239d28ca7733e3d0c181dd4d1f16c563
for (;;)
{
c = **cptr;
@@@ -1196,6 -1198,7 +1204,10 @@@
{
token.push_back(c);
(*cptr)++;
++<<<<<<< HEAD
++=======
+ //i++;
++>>>>>>> 60c6d5d0239d28ca7733e3d0c181dd4d1f16c563
}
}
return (return_value);
diff --cc src/tally.cpp
index 131411e1,8fdb0e6a..00000000
--- a/src/tally.cpp
+++ b/src/tally.cpp
@@@ -798,6 -798,7 +798,10 @@@ build_tally_table(void
*/
int j, k, l, p, save_print_use;
size_t n;
++<<<<<<< HEAD
++=======
+ //int count_tt_pure_phase, count_tt_ss_phase, count_tt_kinetics;
++>>>>>>> 60c6d5d0239d28ca7733e3d0c181dd4d1f16c563
class phase *phase_ptr;
char token[MAX_LENGTH];
const char* cptr;
@@@ -870,6 -871,7 +874,10 @@@
/*
* Count pure phases
*/
++<<<<<<< HEAD
++=======
+ //count_tt_pure_phase = 0;
++>>>>>>> 60c6d5d0239d28ca7733e3d0c181dd4d1f16c563
if (Rxn_pp_assemblage_map.size() > 0)
{
/*
@@@ -902,6 -904,7 +910,10 @@@
/*
* Add to table
*/
++<<<<<<< HEAD
++=======
+ //count_tt_pure_phase++;
++>>>>>>> 60c6d5d0239d28ca7733e3d0c181dd4d1f16c563
n = count_tally_table_columns;
extend_tally_table();
tally_table[n].name = phase_ptr->name;
@@@ -928,6 -931,7 +940,10 @@@
/*
* Add solid-solution pure phases
*/
++<<<<<<< HEAD
++=======
+ //count_tt_ss_phase = 0;
++>>>>>>> 60c6d5d0239d28ca7733e3d0c181dd4d1f16c563
if (Rxn_ss_assemblage_map.size() > 0)
{
/*
@@@ -960,6 -964,7 +976,10 @@@
/*
* Add to table
*/
++<<<<<<< HEAD
++=======
+ //count_tt_ss_phase++;
++>>>>>>> 60c6d5d0239d28ca7733e3d0c181dd4d1f16c563
n = count_tally_table_columns;
extend_tally_table();
tally_table[n].name = phase_ptr->name;
@@@ -977,6 -982,7 +997,10 @@@
/*
* Add kinetic reactants
*/
++<<<<<<< HEAD
++=======
+ //count_tt_kinetics = 0;
++>>>>>>> 60c6d5d0239d28ca7733e3d0c181dd4d1f16c563
if (Rxn_kinetics_map.size() > 0)
{
std::map<int, cxxKinetics>::iterator it;
@@@ -1000,6 -1006,7 +1024,10 @@@
/*
* Add to table
*/
++<<<<<<< HEAD
++=======
+ //count_tt_kinetics++;
++>>>>>>> 60c6d5d0239d28ca7733e3d0c181dd4d1f16c563
n = count_tally_table_columns;
extend_tally_table();
tally_table[n].name = string_hsave(kinetics_comp_ptr->Get_rate_name().c_str());