Consider changing the way you are handling pop-ups. Each browser instance should do it independently from the others. There are many different solutions to handle pop-ups as there are many ways to implement a pop-up.
Please, consider this question for the detailed info.
In short: the main ways to handle pop-ups are:
Using windowHandle:
driver.switchTo().window(subWindowHandler); // switch to popup window
Using Alerts
Alert alert = driver.switchTo().alert();
alert.accept();
Using usual approach when working with elements if pop-up can be accessed this way:
WebElement sign = driver.findElement(By.linkText("Sign in"));
sign.click();
WebElement email_id= driver.findElement(By.id("c_uname"));
email_id.sendKeys("hi");
UPD
One more important thing here is that your code should be able to address appropriate browser instance when handling pop-ups. Otherwise none of the approacehs will work, obviously. This is another big topic, I don't know your implementation of parallelism, so just pay attention to it as well